--- _id: '9684' abstract: - lang: eng text: The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept. article_number: '035001' article_processing_charge: No article_type: original author: - first_name: P S S full_name: Leung, P S S last_name: Leung - first_name: H S full_name: Leung, H S last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A H W full_name: Ngan, A H W last_name: Ngan citation: ama: Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001 apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001 chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001. ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015. ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001. mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001. short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015). date_created: 2021-07-19T09:11:12Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:54Z day: '01' doi: 10.1088/0965-0393/23/3/035001 extern: '1' intvolume: ' 23' issue: '3' language: - iso: eng month: '04' oa_version: None publication: Modelling and Simulation in Materials Science and Engineering publication_identifier: eissn: - 1361-651X issn: - 0965-0393 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Size dependence of yield strength simulated by a dislocation-density function dynamics approach type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 23 year: '2015' ... --- _id: '1566' abstract: - lang: eng text: Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease. acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ' article_number: e1004541 author: - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez citation: ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10). doi:10.1371/journal.pcbi.1004541 apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541 chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541. ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” PLoS Computational Biology, vol. 11, no. 10. Public Library of Science, 2015. ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541. mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004541. short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:52:45Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-02-23T14:05:55Z day: '23' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pcbi.1004541 file: - access_level: open_access checksum: 8b67d729be663bfc9af04bfd94459655 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:21Z date_updated: 2020-07-14T12:45:02Z file_id: '5207' file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf file_size: 1412511 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 11' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5605' pubrep_id: '478' quality_controlled: '1' related_material: record: - id: '9714' relation: research_data status: public scopus_import: 1 status: public title: An exploration of the universe of polyglutamine structures 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: 11 year: '2015' ... --- _id: '9712' article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001 apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001 chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001. ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015. ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001. mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001. short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015). date_created: 2021-07-23T12:00:37Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-02-23T10:09:08Z day: '06' department: - _id: NiBa - _id: CaGu - _id: GaTk doi: 10.1371/journal.pgen.1005639.s001 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1666' relation: used_in_publication status: public status: public title: Other fitness models for comparison & for interacting TFBSs type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9714' article_processing_charge: No author: - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez citation: ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:10.1371/journal.pcbi.1004541.s001 apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001 chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001. ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science , 2015. ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science , 10.1371/journal.pcbi.1004541.s001. mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals. Public Library of Science , 2015, doi:10.1371/journal.pcbi.1004541.s001. short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015). date_created: 2021-07-23T12:05:28Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-02-23T10:04:35Z day: '23' department: - _id: CaHe doi: 10.1371/journal.pcbi.1004541.s001 month: '10' oa_version: Published Version publisher: 'Public Library of Science ' related_material: record: - id: '1566' relation: used_in_publication status: public status: public title: An exploration of the universe of polyglutamine structures - submission to PLOS journals type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9715' article_processing_charge: No author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:10.1371/journal.pone.0126907.s001 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Mathematical inference of the results. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s001 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s001. ieee: B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, 10.1371/journal.pone.0126907.s001. mla: Trubenova, Barbora, et al. Mathematical Inference of the Results. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s001. short: B. Trubenova, S. Novak, R. Hager, (2015). date_created: 2021-07-23T12:11:30Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:15:25Z day: '18' department: - _id: NiBa doi: 10.1371/journal.pone.0126907.s001 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1809' relation: used_in_publication status: public status: public title: Mathematical inference of the results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1993' abstract: - lang: eng text: 'The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. ' acknowledged_ssus: - _id: EM-Fac acknowledgement: "Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript." article_number: '20141976' article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1799). doi:10.1098/rspb.2014.1976 apa: Konrad, M., Grasse, A. V., Tragust, S., & Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.1976 chicago: Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2014.1976. ieee: M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799. The Royal Society, 2015. ista: Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976. mla: Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:10.1098/rspb.2014.1976. short: M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015). date_created: 2018-12-11T11:55:06Z date_published: 2015-01-22T00:00:00Z date_updated: 2023-02-23T14:06:41Z day: '22' department: - _id: SyCr doi: 10.1098/rspb.2014.1976 ec_funded: 1 external_id: pmid: - '25473011' intvolume: ' 282' issue: '1799' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/ month: '01' oa: 1 oa_version: Submitted Version pmid: 1 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: Proceedings of the Royal Society of London Series B Biological Sciences publication_identifier: eissn: - 1471-2954 issn: - 0962-8452 publication_status: published publisher: The Royal Society publist_id: '5090' quality_controlled: '1' related_material: record: - id: '9740' relation: research_data status: public scopus_import: '1' status: public title: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '9742' abstract: - lang: eng text: 'Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.' article_processing_charge: No author: - first_name: Claudia full_name: Westhus, Claudia last_name: Westhus - 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: Edouard full_name: Tourdot, Edouard last_name: Tourdot - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Claudie full_name: Doums, Claudie last_name: Doums - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:10.5061/dryad.7kc79' apa: 'Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., & Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. https://doi.org/10.5061/dryad.7kc79' chicago: 'Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. https://doi.org/10.5061/dryad.7kc79.' ieee: 'C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.' ista: 'Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, 10.5061/dryad.7kc79.' mla: 'Westhus, Claudia, et al. Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant. Dryad, 2015, doi:10.5061/dryad.7kc79.' short: C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015). date_created: 2021-07-28T08:52:53Z date_published: 2015-07-09T00:00:00Z date_updated: 2023-02-23T10:30:52Z day: '09' department: - _id: SyCr doi: 10.5061/dryad.7kc79 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.7kc79 month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2161' relation: used_in_publication status: public status: public title: 'Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9765' article_processing_charge: No author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Tugce full_name: Batur, Tugce last_name: Batur - first_name: Aysegul full_name: Guvenek, Aysegul last_name: Guvenek - first_name: Dilay Hazal full_name: Ayhan, Dilay Hazal last_name: Ayhan - first_name: Erdal full_name: Toprak, Erdal last_name: Toprak - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:10.1371/journal.pbio.1002299.s008 apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., & Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s008 chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s008. ieee: G. Chevereau et al., “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015. ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, 10.1371/journal.pbio.1002299.s008. mla: Chevereau, Guillaume, et al. Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s008. short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015). date_created: 2021-08-03T07:05:16Z date_published: 2015-11-18T00:00:00Z date_updated: 2023-02-23T10:07:02Z day: '18' department: - _id: ToBo doi: 10.1371/journal.pbio.1002299.s008 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1619' relation: used_in_publication status: public status: public title: Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '12630' abstract: - lang: eng text: "The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n" article_processing_charge: No article_type: original author: - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: W.W. full_name: Immerzeel, W.W. last_name: Immerzeel - first_name: E.S. full_name: Miles, E.S. last_name: Miles - first_name: L. full_name: Petersen, L. last_name: Petersen - first_name: M. full_name: Heynen, M. last_name: Heynen - first_name: J.M. full_name: Shea, J.M. last_name: Shea - first_name: D. full_name: Stumm, D. last_name: Stumm - first_name: S. full_name: Joshi, S. last_name: Joshi - first_name: A. full_name: Shrestha, A. last_name: Shrestha citation: ama: Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 2015;78(4):94-111. doi:10.1016/j.advwatres.2015.01.013 apa: Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2015.01.013 chicago: Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources. Elsevier, 2015. https://doi.org/10.1016/j.advwatres.2015.01.013. ieee: S. Ragettli et al., “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” Advances in Water Resources, vol. 78, no. 4. Elsevier, pp. 94–111, 2015. ista: Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111. mla: Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” Advances in Water Resources, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:10.1016/j.advwatres.2015.01.013. short: S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111. date_created: 2023-02-20T08:16:21Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-24T09:28:04Z day: '01' doi: 10.1016/j.advwatres.2015.01.013 extern: '1' intvolume: ' 78' issue: '4' keyword: - Water Science and Technology language: - iso: eng month: '04' oa_version: None page: 94-111 publication: Advances in Water Resources publication_identifier: issn: - 0309-1708 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2015' ... --- _id: '12628' abstract: - lang: eng text: Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Christa full_name: Stephan, Christa last_name: Stephan - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Sam full_name: Herreid, Sam last_name: Herreid - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel - first_name: Tobias full_name: Bolch, Tobias last_name: Bolch citation: ama: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 2015;61(226):373-386. doi:10.3189/2015jog13j237 apa: Pellicciotti, F., Stephan, C., Miles, E., Herreid, S., Immerzeel, W. W., & Bolch, T. (2015). Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog13j237 chicago: Pellicciotti, Francesca, Christa Stephan, Evan Miles, Sam Herreid, Walter W. Immerzeel, and Tobias Bolch. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog13j237. ieee: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W. W. Immerzeel, and T. Bolch, “Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999,” Journal of Glaciology, vol. 61, no. 226. International Glaciological Society, pp. 373–386, 2015. ista: Pellicciotti F, Stephan C, Miles E, Herreid S, Immerzeel WW, Bolch T. 2015. Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999. Journal of Glaciology. 61(226), 373–386. mla: Pellicciotti, Francesca, et al. “Mass-Balance Changes of the Debris-Covered Glaciers in the Langtang Himal, Nepal, from 1974 to 1999.” Journal of Glaciology, vol. 61, no. 226, International Glaciological Society, 2015, pp. 373–86, doi:10.3189/2015jog13j237. short: F. Pellicciotti, C. Stephan, E. Miles, S. Herreid, W.W. Immerzeel, T. Bolch, Journal of Glaciology 61 (2015) 373–386. date_created: 2023-02-20T08:16:11Z date_published: 2015-03-01T00:00:00Z date_updated: 2023-02-24T09:35:21Z day: '01' doi: 10.3189/2015jog13j237 extern: '1' intvolume: ' 61' issue: '226' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG13J237 month: '03' oa: 1 oa_version: Published Version page: 373-386 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '12631' abstract: - lang: eng text: Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines. article_processing_charge: No article_type: original author: - first_name: A. full_name: Ayala, A. last_name: Ayala - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: J. M. full_name: Shea, J. M. last_name: Shea citation: ama: 'Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137' apa: 'Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137' chicago: 'Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137.' ieee: 'A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015.' ista: 'Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.' mla: 'Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.' short: 'A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.' date_created: 2023-02-20T08:16:28Z date_published: 2015-04-18T00:00:00Z date_updated: 2023-02-24T09:16:26Z day: '18' doi: 10.1002/2015jd023137 extern: '1' intvolume: ' 120' issue: '8' keyword: - Space and Planetary Science - Earth and Planetary Sciences (miscellaneous) - Atmospheric Science - Geophysics language: - iso: eng month: '04' oa_version: Published Version page: 3139-3157 publication: 'Journal of Geophysical Research: Atmospheres' publication_identifier: eissn: - 2169-8996 issn: - 2169-897X publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: 'Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2015' ... --- _id: '12629' abstract: - lang: eng text: Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region. article_processing_charge: No article_type: original author: - first_name: J.M. full_name: Shea, J.M. last_name: Shea - first_name: P. full_name: Wagnon, P. last_name: Wagnon - first_name: W.W. full_name: Immerzeel, W.W. last_name: Immerzeel - first_name: R. full_name: Biron, R. last_name: Biron - first_name: F. full_name: Brun, F. last_name: Brun - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417 apa: Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417 chicago: Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417. ieee: J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015. ista: Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200. mla: Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417. short: J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200. date_created: 2023-02-20T08:16:17Z date_published: 2015-04-18T00:00:00Z date_updated: 2023-02-24T09:30:42Z day: '18' doi: 10.1080/07900627.2015.1020417 extern: '1' intvolume: ' 31' issue: '2' keyword: - Water Science and Technology - Development language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1080/07900627.2015.1020417 month: '04' oa: 1 oa_version: Published Version page: 174-200 publication: International Journal of Water Resources Development publication_identifier: eissn: - 1360-0648 issn: - 0790-0627 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '12626' abstract: - lang: eng text: Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%. article_processing_charge: No article_type: original author: - first_name: Jakob F. full_name: Steiner, Jakob F. last_name: Steiner - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel - first_name: Tim D. full_name: Reid, Tim D. last_name: Reid citation: ama: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194 apa: Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194 chicago: Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194. ieee: J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015. ista: Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907. mla: Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194. short: J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907. date_created: 2023-02-20T08:16:01Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-24T09:43:14Z day: '01' doi: 10.3189/2015jog14j194 extern: '1' intvolume: ' 61' issue: '229' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG14J194 month: '07' oa: 1 oa_version: Published Version page: 889-907 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '12627' abstract: - lang: eng text: Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known. article_processing_charge: No article_type: original author: - first_name: Sam full_name: Herreid, Sam last_name: Herreid - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Alvaro full_name: Ayala, Alvaro last_name: Ayala - first_name: Anna full_name: Chesnokova, Anna last_name: Chesnokova - first_name: Christian full_name: Kienholz, Christian last_name: Kienholz - first_name: Joseph full_name: Shea, Joseph last_name: Shea - first_name: Arun full_name: Shrestha, Arun last_name: Shrestha citation: ama: Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227 apa: Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227 chicago: Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227. ieee: S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015. ista: Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536. mla: Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227. short: S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536. date_created: 2023-02-20T08:16:06Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-24T09:40:30Z day: '01' doi: 10.3189/2015jog14j227 extern: '1' intvolume: ' 61' issue: '227' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3189/2015JoG14J227 month: '05' oa: 1 oa_version: Published Version page: 524-536 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: International Glaciological Society quality_controlled: '1' scopus_import: '1' status: public title: Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '1618' abstract: - lang: eng text: CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed. article_processing_charge: No author: - first_name: Christopher full_name: Veldkamp, Christopher last_name: Veldkamp - first_name: Eva full_name: Kiermaier, Eva id: 3EB04B78-F248-11E8-B48F-1D18A9856A87 last_name: Kiermaier orcid: 0000-0001-6165-5738 - first_name: Skylar full_name: Gabel Eissens, Skylar last_name: Gabel Eissens - first_name: Miranda full_name: Gillitzer, Miranda last_name: Gillitzer - first_name: David full_name: Lippner, David last_name: Lippner - first_name: Frank full_name: Disilvio, Frank last_name: Disilvio - first_name: Casey full_name: Mueller, Casey last_name: Mueller - first_name: Paeton full_name: Wantuch, Paeton last_name: Wantuch - first_name: Gary full_name: Chaffee, Gary last_name: Chaffee - first_name: Michael full_name: Famiglietti, Michael last_name: Famiglietti - first_name: Danielle full_name: Zgoba, Danielle last_name: Zgoba - first_name: Asha full_name: Bailey, Asha last_name: Bailey - first_name: Yaya full_name: Bah, Yaya last_name: Bah - first_name: Samantha full_name: Engebretson, Samantha last_name: Engebretson - first_name: David full_name: Graupner, David last_name: Graupner - first_name: Emily full_name: Lackner, Emily last_name: Lackner - first_name: Vincent full_name: Larosa, Vincent last_name: Larosa - first_name: Tysha full_name: Medeiros, Tysha last_name: Medeiros - first_name: Michael full_name: Olson, Michael last_name: Olson - first_name: Andrew full_name: Phillips, Andrew last_name: Phillips - first_name: Harley full_name: Pyles, Harley last_name: Pyles - first_name: Amanda full_name: Richard, Amanda last_name: Richard - first_name: Scott full_name: Schoeller, Scott last_name: Schoeller - first_name: Boris full_name: Touzeau, Boris last_name: Touzeau - first_name: Larry full_name: Williams, Larry last_name: Williams - 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: Francis full_name: Peterson, Francis last_name: Peterson citation: ama: Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560 apa: Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560 chicago: Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560. ieee: C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015. ista: Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166. mla: Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560. short: C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166. date_created: 2018-12-11T11:53:03Z date_published: 2015-06-26T00:00:00Z date_updated: 2023-03-30T11:32:57Z day: '26' department: - _id: MiSi doi: 10.1021/acs.biochem.5b00560 ec_funded: 1 external_id: pmid: - '26115234' intvolume: ' 54' issue: '27' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/ month: '06' oa: 1 oa_version: Submitted Version page: 4163 - 4166 pmid: 1 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Biochemistry publication_status: published publisher: American Chemical Society publist_id: '5548' quality_controlled: '1' scopus_import: '1' status: public title: Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ... --- _id: '12881' acknowledgement: This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734). article_processing_charge: No author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Eckehard full_name: Olbrich, Eckehard last_name: Olbrich citation: ama: 'Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018' apa: 'Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018' chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018. ieee: G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78. ista: 'Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.' mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018. short: G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78. conference: end_date: 2015-07-24 location: York, United Kingdom name: 'ECAL: European Conference on Artificial Life' start_date: 2015-07-20 date_created: 2023-04-30T22:01:07Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-05-02T07:06:21Z day: '01' ddc: - '000' department: - _id: ChLa doi: 10.7551/978-0-262-33027-5-ch018 ec_funded: 1 file: - access_level: open_access checksum: 880eabe59c9df12f06a882aa1bc4e600 content_type: application/pdf creator: dernst date_created: 2023-05-02T07:02:59Z date_updated: 2023-05-02T07:02:59Z file_id: '12882' file_name: 2015_ECAL_Martius.pdf file_size: 1674241 relation: main_file success: 1 file_date_updated: 2023-05-02T07:02:59Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '78' project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Proceedings of the 13th European Conference on Artificial Life publication_identifier: isbn: - '9780262330275' publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying self-organizing behavior of autonomous robots 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 year: '2015' ... --- _id: '12196' abstract: - lang: eng text: SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity. acknowledgement: "This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript." article_processing_charge: No article_type: original author: - first_name: Kaeli C.M. full_name: Johnson, Kaeli C.M. last_name: Johnson - first_name: Shitou full_name: Xia, Shitou last_name: Xia - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Xin full_name: Li, Xin last_name: Li citation: ama: Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087 apa: Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087 chicago: Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087. ieee: K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015. ista: Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623. mla: Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087. short: K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623. date_created: 2023-01-16T09:20:22Z date_published: 2015-08-01T00:00:00Z date_updated: 2023-05-08T11:03:23Z department: - _id: XiFe doi: 10.1093/pcp/pcv087 extern: '1' external_id: pmid: - '26063389' intvolume: ' 56' issue: '8' keyword: - Cell Biology - Plant Science - Physiology - General Medicine language: - iso: eng month: '08' oa_version: None page: 1616-1623 pmid: 1 publication: Plant and Cell Physiology publication_identifier: issn: - 0032-0781 - 1471-9053 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2015' ... --- _id: '13392' abstract: - lang: eng text: The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution. article_processing_charge: No article_type: original author: - first_name: Hui full_name: Zhao, Hui last_name: Zhao - first_name: Soumyo full_name: Sen, Soumyo last_name: Sen - first_name: T. full_name: Udayabhaskararao, T. last_name: Udayabhaskararao - first_name: Michał full_name: Sawczyk, Michał last_name: Sawczyk - first_name: Kristina full_name: Kučanda, Kristina last_name: Kučanda - first_name: Debasish full_name: Manna, Debasish last_name: Manna - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Ji-Woong full_name: Lee, Ji-Woong last_name: Lee - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 2015;11:82-88. doi:10.1038/nnano.2015.256 apa: Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D., … Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256 chicago: Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda, Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256. ieee: H. Zhao et al., “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11. Springer Nature, pp. 82–88, 2015. ista: Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK, Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88. mla: Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature, 2015, pp. 82–88, doi:10.1038/nnano.2015.256. short: H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K. Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88. date_created: 2023-08-01T09:44:04Z date_published: 2015-11-23T00:00:00Z date_updated: 2023-08-07T12:55:46Z day: '23' doi: 10.1038/nnano.2015.256 extern: '1' external_id: pmid: - '26595335' intvolume: ' 11' keyword: - Electrical and Electronic Engineering - Condensed Matter Physics - General Materials Science - Biomedical Engineering - Atomic and Molecular Physics - and Optics - Bioengineering language: - iso: eng month: '11' oa_version: None page: 82-88 pmid: 1 publication: Nature Nanotechnology publication_identifier: eissn: - 1748-3395 issn: - 1748-3387 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '13394' abstract: - lang: eng text: The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time. article_processing_charge: No article_type: original author: - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Dipak full_name: Samanta, Dipak last_name: Samanta - first_name: Ron full_name: Leizrowice, Ron last_name: Leizrowice - first_name: Baruch full_name: Margulis, Baruch last_name: Margulis - first_name: Hui full_name: Zhao, Hui last_name: Zhao - first_name: Martin full_name: Börner, Martin last_name: Börner - first_name: T. full_name: Udayabhaskararao, T. last_name: Udayabhaskararao - first_name: Debasish full_name: Manna, Debasish last_name: Manna - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303 apa: Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner, M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303 chicago: Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao, Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2303. ieee: P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652, 2015. ista: Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 7, 646–652. mla: Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52, doi:10.1038/nchem.2303. short: P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T. Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652. date_created: 2023-08-01T09:44:33Z date_published: 2015-07-20T00:00:00Z date_updated: 2023-08-07T13:00:15Z day: '20' doi: 10.1038/nchem.2303 extern: '1' external_id: pmid: - '26201741' intvolume: ' 7' keyword: - General Chemical Engineering - General Chemistry language: - iso: eng month: '07' oa_version: None page: 646-652 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Light-controlled self-assembly of non-photoresponsive nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '13393' abstract: - lang: eng text: Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light. article_processing_charge: No article_type: original author: - first_name: Debasish full_name: Manna, Debasish last_name: Manna - first_name: Thumu full_name: Udayabhaskararao, Thumu last_name: Udayabhaskararao - first_name: Hui full_name: Zhao, Hui last_name: Zhao - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419 apa: Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419 chicago: Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419. ieee: D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015. ista: Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 54(42), 12394–12397. mla: Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419. short: D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397. date_created: 2023-08-01T09:44:19Z date_published: 2015-10-01T00:00:00Z date_updated: 2023-08-07T12:58:29Z day: '01' doi: 10.1002/anie.201502419 extern: '1' external_id: pmid: - '25959725' intvolume: ' 54' issue: '42' keyword: - General Chemistry - Catalysis language: - iso: eng month: '10' oa_version: None page: 12394-12397 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ... --- _id: '13395' abstract: - lang: eng text: Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate. article_processing_charge: No article_type: original author: - first_name: Ji-Woong full_name: Lee, Ji-Woong last_name: Lee - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 2015;51(11):2036-2039. doi:10.1039/c4cc08541h apa: Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h chicago: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h. ieee: J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” Chemical Communications, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015. ista: Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039. mla: Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h. short: J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039. date_created: 2023-08-01T09:44:48Z date_published: 2015-11-18T00:00:00Z date_updated: 2023-08-07T13:01:53Z day: '18' doi: 10.1039/c4cc08541h extern: '1' external_id: pmid: - '25417754' intvolume: ' 51' issue: '11' keyword: - Materials Chemistry - Metals and Alloys - Surfaces - Coatings and Films - General Chemistry - Ceramics and Composites - Electronic - Optical and Magnetic Materials - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/C4CC08541H month: '11' oa: 1 oa_version: Published Version page: 2036-2039 pmid: 1 publication: Chemical Communications publication_identifier: eissn: - 1364-548X issn: - 1359-7345 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2015' ... --- _id: '13396' abstract: - lang: eng text: 'Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs.' article_processing_charge: No article_type: original author: - first_name: Thomas full_name: Moldt, Thomas last_name: Moldt - first_name: Daniel full_name: Brete, Daniel last_name: Brete - first_name: Daniel full_name: Przyrembel, Daniel last_name: Przyrembel - first_name: Sanjib full_name: Das, Sanjib last_name: Das - first_name: Joel R. full_name: Goldman, Joel R. last_name: Goldman - first_name: Pintu K. full_name: Kundu, Pintu K. last_name: Kundu - first_name: Cornelius full_name: Gahl, Cornelius last_name: Gahl - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Martin full_name: Weinelt, Martin last_name: Weinelt citation: ama: Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057. doi:10.1021/la504291n apa: Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K., … Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. American Chemical Society. https://doi.org/10.1021/la504291n chicago: Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman, Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n. ieee: T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015. ista: Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057. mla: Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n. short: T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl, R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057. date_created: 2023-08-01T09:45:02Z date_published: 2015-01-27T00:00:00Z date_updated: 2023-08-07T13:05:04Z day: '27' doi: 10.1021/la504291n extern: '1' external_id: pmid: - '25544061' intvolume: ' 31' issue: '3' keyword: - Electrochemistry - Spectroscopy - Surfaces and Interfaces - Condensed Matter Physics - General Materials Science language: - iso: eng month: '01' oa_version: None page: 1048-1057 pmid: 1 publication: Langmuir publication_identifier: eissn: - 1520-5827 issn: - 0743-7463 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '13397' abstract: - lang: eng text: Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light. article_processing_charge: No article_type: original author: - first_name: Gurvinder full_name: Singh, Gurvinder last_name: Singh - first_name: Henry full_name: Chan, Henry last_name: Chan - first_name: T. full_name: Udayabhaskararao, T. last_name: Udayabhaskararao - first_name: Elijah full_name: Gelman, Elijah last_name: Gelman - first_name: Davide full_name: Peddis, Davide last_name: Peddis - first_name: Artem full_name: Baskin, Artem last_name: Baskin - first_name: Gregory full_name: Leitus, Gregory last_name: Leitus - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b apa: Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b chicago: Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b. ieee: G. Singh et al., “Magnetic field-induced self-assembly of iron oxide nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015. ista: Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421. mla: Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:10.1039/c4fd00265b. short: G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421. date_created: 2023-08-01T09:45:17Z date_published: 2015-01-02T00:00:00Z date_updated: 2023-08-07T13:06:23Z day: '02' doi: 10.1039/c4fd00265b extern: '1' external_id: pmid: - '25920522' intvolume: ' 181' keyword: - Physical and Theoretical Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/C4FD00265B month: '01' oa: 1 oa_version: Published Version page: 403-421 pmid: 1 publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Magnetic field-induced self-assembly of iron oxide nanocubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 181 year: '2015' ... --- _id: '13398' article_processing_charge: No article_type: letter_note author: - first_name: Yugang full_name: Sun, Yugang last_name: Sun - first_name: Leonardo full_name: Scarabelli, Leonardo last_name: Scarabelli - first_name: Nicholas full_name: Kotov, Nicholas last_name: Kotov - first_name: Moritz full_name: Tebbe, Moritz last_name: Tebbe - first_name: Xiao-Min full_name: Lin, Xiao-Min last_name: Lin - first_name: Ward full_name: Brullot, Ward last_name: Brullot - first_name: Lucio full_name: Isa, Lucio last_name: Isa - first_name: Peter full_name: Schurtenberger, Peter last_name: Schurtenberger - first_name: Helmuth full_name: Moehwald, Helmuth last_name: Moehwald - first_name: Igor full_name: Fedin, Igor last_name: Fedin - first_name: Orlin full_name: Velev, Orlin last_name: Velev - first_name: Damien full_name: Faivre, Damien last_name: Faivre - first_name: Christopher full_name: Sorensen, Christopher last_name: Sorensen - first_name: Régine full_name: Perzynski, Régine last_name: Perzynski - first_name: Munish full_name: Chanana, Munish last_name: Chanana - first_name: Zhihai full_name: Li, Zhihai last_name: Li - first_name: Fernando full_name: Bresme, Fernando last_name: Bresme - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Emre full_name: Firlar, Emre last_name: Firlar - first_name: David full_name: Schiffrin, David last_name: Schiffrin - first_name: Joao Batista full_name: Souza Junior, Joao Batista last_name: Souza Junior - first_name: Andreas full_name: Fery, Andreas last_name: Fery - first_name: Elena full_name: Shevchenko, Elena last_name: Shevchenko - first_name: Ozgur full_name: Tarhan, Ozgur last_name: Tarhan - first_name: Armand Paul full_name: Alivisatos, Armand Paul last_name: Alivisatos - first_name: Sabrina full_name: Disch, Sabrina last_name: Disch - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Suvojit full_name: Ghosh, Suvojit last_name: Ghosh citation: ama: 'Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g' apa: 'Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g' chicago: 'Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.' ieee: 'Y. Sun et al., “Field-assisted self-assembly process: General discussion,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015.' ista: 'Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M, Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly process: General discussion. Faraday Discussions. 181, 463–479.' mla: 'Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:10.1039/c5fd90041g.' short: Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa, P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R. Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B. Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R. Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479. date_created: 2023-08-01T09:45:29Z date_published: 2015-07-07T00:00:00Z date_updated: 2023-08-08T07:16:20Z day: '07' doi: 10.1039/c5fd90041g extern: '1' external_id: pmid: - '26149295' intvolume: ' 181' keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '07' oa_version: None page: 463-479 pmid: 1 publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Field-assisted self-assembly process: General discussion' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 181 year: '2015' ... --- _id: '14017' abstract: - lang: eng text: The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results. article_number: '023421' article_processing_charge: No article_type: original author: - first_name: Song Bin full_name: Zhang, Song Bin last_name: Zhang - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Peter M. full_name: Kraus, Peter M. last_name: Kraus - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner - first_name: Nina full_name: Rohringer, Nina last_name: Rohringer citation: ama: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421 apa: Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.91.023421 chicago: Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421. ieee: S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” Physical Review A, vol. 91, no. 2. American Physical Society, 2015. ista: Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421. mla: Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421. short: S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015). date_created: 2023-08-10T06:38:10Z date_published: 2015-02-19T00:00:00Z date_updated: 2023-08-22T08:56:34Z day: '19' doi: 10.1103/physreva.91.023421 extern: '1' external_id: arxiv: - '1504.03933' intvolume: ' 91' issue: '2' keyword: - Atomic and Molecular Physics - and Optics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.03933 month: '02' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 1094-1622 issn: - 1050-2947 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '14016' abstract: - lang: eng text: All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies. article_number: '7039' article_processing_charge: No article_type: original author: - first_name: P. M. full_name: Kraus, P. M. last_name: Kraus - first_name: O. I. full_name: Tolstikhin, O. I. last_name: Tolstikhin - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: A. full_name: Rupenyan, A. last_name: Rupenyan - first_name: J. full_name: Schneider, J. last_name: Schneider - first_name: C. Z. full_name: Bisgaard, C. Z. last_name: Bisgaard - first_name: T. full_name: Morishita, T. last_name: Morishita - first_name: F. full_name: Jensen, F. last_name: Jensen - first_name: L. B. full_name: Madsen, L. B. last_name: Madsen - first_name: H. J. full_name: Wörner, H. J. last_name: Wörner citation: ama: Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039 apa: Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039 chicago: Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039. ieee: P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015. ista: Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039. mla: Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039. short: P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015). date_created: 2023-08-10T06:38:01Z date_published: 2015-05-05T00:00:00Z date_updated: 2023-08-22T08:52:56Z day: '05' doi: 10.1038/ncomms8039 extern: '1' external_id: pmid: - '25940229' intvolume: ' 6' keyword: - General Physics and Astronomy - General Biochemistry - Genetics and Molecular Biology - General Chemistry - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/ncomms8039 month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Observation of laser-induced electronic structure in oriented polyatomic molecules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '14013' abstract: - lang: eng text: The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes. article_processing_charge: No article_type: original author: - first_name: P. M. full_name: Kraus, P. M. last_name: Kraus - first_name: B. full_name: Mignolet, B. last_name: Mignolet - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: A. full_name: Rupenyan, A. last_name: Rupenyan - first_name: L. full_name: Horný, L. last_name: Horný - first_name: E. F. full_name: Penka, E. F. last_name: Penka - first_name: G. full_name: Grassi, G. last_name: Grassi - first_name: O. I. full_name: Tolstikhin, O. I. last_name: Tolstikhin - first_name: J. full_name: Schneider, J. last_name: Schneider - first_name: F. full_name: Jensen, F. last_name: Jensen - first_name: L. B. full_name: Madsen, L. B. last_name: Madsen - first_name: A. D. full_name: Bandrauk, A. D. last_name: Bandrauk - first_name: F. full_name: Remacle, F. last_name: Remacle - first_name: H. J. full_name: Wörner, H. J. last_name: Wörner citation: ama: Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 2015;350(6262):790-795. doi:10.1126/science.aab2160 apa: Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aab2160 chicago: Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L. Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aab2160. ieee: P. M. Kraus et al., “Measurement and laser control of attosecond charge migration in ionized iodoacetylene,” Science, vol. 350, no. 6262. American Association for the Advancement of Science, pp. 790–795, 2015. ista: Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 350(6262), 790–795. mla: Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160. short: P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Science 350 (2015) 790–795. date_created: 2023-08-10T06:37:35Z date_published: 2015-10-22T00:00:00Z date_updated: 2023-08-22T08:47:39Z day: '22' doi: 10.1126/science.aab2160 extern: '1' external_id: pmid: - '26494175' intvolume: ' 350' issue: '6262' keyword: - Multidisciplinary language: - iso: eng month: '10' oa_version: None page: 790-795 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: Measurement and laser control of attosecond charge migration in ionized iodoacetylene type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 350 year: '2015' ... --- _id: '14015' abstract: - lang: eng text: We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes. article_number: '112136' article_processing_charge: No article_type: original author: - first_name: P M full_name: Kraus, P M last_name: Kraus - first_name: B full_name: Mignolet, B last_name: Mignolet - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: A full_name: Rupenyan, A last_name: Rupenyan - first_name: L full_name: Horný, L last_name: Horný - first_name: E F full_name: Penka, E F last_name: Penka - first_name: O I full_name: Tolstikhin, O I last_name: Tolstikhin - first_name: J full_name: Schneider, J last_name: Schneider - first_name: F full_name: Jensen, F last_name: Jensen - first_name: L B full_name: Madsen, L B last_name: Madsen - first_name: A D full_name: Bandrauk, A D last_name: Bandrauk - first_name: F full_name: Remacle, F last_name: Remacle - first_name: H J full_name: Wörner, H J last_name: Wörner citation: ama: 'Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112136' apa: 'Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112136' chicago: 'Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný, E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112136.' ieee: 'P. M. Kraus et al., “Attosecond charge migration and its laser control,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.' ista: 'Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 635(11), 112136.' mla: 'Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.” Journal of Physics: Conference Series, vol. 635, no. 11, 112136, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112136.' short: 'P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).' date_created: 2023-08-10T06:37:53Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-08-22T08:49:14Z day: '01' doi: 10.1088/1742-6596/635/11/112136 extern: '1' intvolume: ' 635' issue: '11' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1088/1742-6596/635/11/112136 month: '07' oa: 1 oa_version: Published Version publication: 'Journal of Physics: Conference Series' publication_identifier: eissn: - 1742-6596 issn: - 1742-6588 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Attosecond charge migration and its laser control type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 635 year: '2015' ... --- _id: '14014' abstract: - lang: eng text: We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons. article_number: '112135' article_processing_charge: No article_type: original author: - first_name: Samuel G full_name: Walt, Samuel G last_name: Walt - first_name: N Bhargava full_name: Ram, N Bhargava last_name: Ram - first_name: Aaron full_name: von Conta, Aaron last_name: von Conta - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Marcos full_name: Atala, Marcos last_name: Atala - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 2015;635(11). doi:10.1088/1742-6596/635/11/112135' apa: 'Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., & Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. IOP Publishing. https://doi.org/10.1088/1742-6596/635/11/112135' chicago: 'Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva, Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series. IOP Publishing, 2015. https://doi.org/10.1088/1742-6596/635/11/112135.' ieee: 'S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J. Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography,” Journal of Physics: Conference Series, vol. 635, no. 11. IOP Publishing, 2015.' ista: 'Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 635(11), 112135.' mla: 'Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135.' short: 'S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).' date_created: 2023-08-10T06:37:44Z date_published: 2015-11-01T00:00:00Z date_updated: 2023-08-22T08:51:33Z day: '01' doi: 10.1088/1742-6596/635/11/112135 extern: '1' intvolume: ' 635' issue: '11' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1088/1742-6596/635/11/112135 month: '11' oa: 1 oa_version: Published Version publication: 'Journal of Physics: Conference Series' publication_identifier: eissn: - 1742-6596 issn: - 1742-6588 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 635 year: '2015' ... --- _id: '9719' abstract: - lang: eng text: Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance. article_processing_charge: No author: - first_name: Sébastien full_name: Wielgoss, Sébastien last_name: Wielgoss - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Anna M. full_name: Bischofberger, Anna M. last_name: Bischofberger - first_name: Alex R. full_name: Hall, Alex R. last_name: Hall citation: ama: 'Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:10.5061/dryad.cj910' apa: 'Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. https://doi.org/10.5061/dryad.cj910' chicago: 'Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. https://doi.org/10.5061/dryad.cj910.' ieee: 'S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.' ista: 'Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad, 10.5061/dryad.cj910.' mla: 'Wielgoss, Sébastien, et al. Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria. Dryad, 2015, doi:10.5061/dryad.cj910.' short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015). date_created: 2021-07-26T08:44:04Z date_published: 2015-12-21T00:00:00Z date_updated: 2023-09-05T13:46:04Z day: '21' department: - _id: CaGu doi: 10.5061/dryad.cj910 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.cj910 month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '5749' relation: used_in_publication status: public status: public title: 'Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1401' abstract: - lang: eng text: 'The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views.' acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 citation: ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:10.15479/at:ista:1401' apa: 'Sharmanska, V. (2015). Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1401' chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/at:ista:1401.' ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.' ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.' mla: 'Sharmanska, Viktoriia. Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views. Institute of Science and Technology Austria, 2015, doi:10.15479/at:ista:1401.' short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.' date_created: 2018-12-11T11:51:48Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-09-07T11:40:11Z day: '01' ddc: - '000' degree_awarded: PhD department: - _id: ChLa - _id: GradSch doi: 10.15479/at:ista:1401 file: - access_level: open_access checksum: 3605b402bb6934e09ae4cf672c84baf7 content_type: application/pdf creator: dernst date_created: 2021-02-22T11:33:17Z date_updated: 2021-02-22T11:33:17Z file_id: '9177' file_name: 2015_Thesis_Sharmanska.pdf file_size: 7964342 relation: main_file success: 1 - access_level: closed checksum: e37593b3ee75bf3180629df2d6ca8f4e content_type: application/pdf creator: cchlebak date_created: 2021-11-16T14:40:45Z date_updated: 2021-11-17T13:47:24Z file_id: '10297' file_name: 2015_Thesis_Sharmanska_pdfa.pdf file_size: 7372241 relation: main_file file_date_updated: 2021-11-17T13:47:24Z has_accepted_license: '1' language: - iso: eng main_file_link: - url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf month: '04' oa: 1 oa_version: Published Version page: '144' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5806' status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: 'Learning with attributes for object recognition: Parametric and non-parametrics views' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2015' ... --- _id: '1709' abstract: - lang: eng text: The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards. acknowledgement: 'This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.' article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041 apa: Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015). Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041 chicago: Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rspb.2015.1041. ieee: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015. ista: Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812). mla: Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041. short: J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015). date_created: 2018-12-11T11:53:35Z date_published: 2015-07-15T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '15' department: - _id: KrCh doi: 10.1098/rspb.2015.1041 external_id: pmid: - '26180069' intvolume: ' 282' issue: '1812' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/ month: '07' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: Royal Society publist_id: '5425' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: Biological auctions with multiple rewards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 282 year: '2015' ... --- _id: '1400' abstract: - lang: eng text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 citation: ama: Reiter J. The subclonal evolution of cancer. 2015. apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science and Technology Austria. chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015. ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015. ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria. mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science and Technology Austria, 2015. short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015. date_created: 2018-12-11T11:51:48Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-09-07T11:40:44Z day: '01' degree_awarded: PhD department: - _id: KrCh language: - iso: eng month: '04' oa_version: None page: '183' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5807' related_material: record: - id: '1709' relation: part_of_dissertation status: public - id: '2000' relation: part_of_dissertation status: public - id: '2247' relation: part_of_dissertation status: public - id: '2816' relation: part_of_dissertation status: public - id: '2858' relation: part_of_dissertation status: public - id: '3157' relation: part_of_dissertation status: public - id: '3260' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: The subclonal evolution of cancer type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2015' ... --- _id: '1792' abstract: - lang: eng text: Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology. acknowledgement: F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation. author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 - first_name: Anne full_name: Svane, Anne last_name: Svane citation: ama: Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002 apa: Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002 chicago: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002. ieee: F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797, 2015. ista: Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797. mla: Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002. short: F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797. date_created: 2018-12-11T11:54:02Z date_published: 2015-12-01T00:00:00Z date_updated: 2023-09-07T11:41:25Z day: '01' department: - _id: HeEd doi: 10.1016/j.jco.2015.06.002 intvolume: ' 31' issue: '6' language: - iso: eng month: '12' oa_version: None page: 773 - 797 publication: Journal of Complexity publication_status: published publisher: Academic Press publist_id: '5320' quality_controlled: '1' related_material: record: - id: '1399' relation: dissertation_contains status: public scopus_import: 1 status: public title: A Koksma-Hlawka inequality for general discrepancy systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2015' ... --- _id: '1399' abstract: - lang: eng text: This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Pausinger F. On the approximation of intrinsic volumes. 2015. apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute of Science and Technology Austria. chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015. ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015. ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria. mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute of Science and Technology Austria, 2015. short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015. date_created: 2018-12-11T11:51:48Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-09-07T11:41:25Z day: '01' degree_awarded: PhD department: - _id: HeEd language: - iso: eng month: '06' oa_version: None page: '144' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5808' related_material: record: - id: '1662' relation: part_of_dissertation status: public - id: '1792' relation: part_of_dissertation status: public - id: '2255' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: On the approximation of intrinsic volumes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2015' ... --- _id: '1666' abstract: - lang: eng text: Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics. author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639 apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639 chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639. ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015. ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11). mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639. short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015). date_created: 2018-12-11T11:53:21Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-09-07T11:53:49Z day: '06' ddc: - '576' department: - _id: NiBa - _id: CaGu - _id: GaTk doi: 10.1371/journal.pgen.1005639 ec_funded: 1 file: - access_level: open_access checksum: a4e72fca5ccf40ddacf4d08c8e46b554 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:58Z date_updated: 2020-07-14T12:45:10Z file_id: '4657' file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf file_size: 2580778 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' intvolume: ' 11' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '5483' pubrep_id: '463' quality_controlled: '1' related_material: record: - id: '9712' relation: research_data status: public - id: '1131' relation: dissertation_contains status: public scopus_import: 1 status: public title: Dynamics of transcription factor binding site evolution 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: 11 year: '2015' ... --- _id: '1502' abstract: - lang: eng text: We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system. acknowledgement: "This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation, grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence." alternative_title: - 'Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering ' author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic citation: ama: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175' apa: 'Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. https://doi.org/10.1145/2737166.2737175' chicago: Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. https://doi.org/10.1145/2737166.2737175. ieee: 'N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.' ista: 'Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.' mla: Beneš, Nikola, et al. Complete Composition Operators for IOCO-Testing Theory. ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175. short: N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110. conference: end_date: 2015-05-08 location: Montreal, QC, Canada name: 'CBSE: Component-Based Software Engineering ' start_date: 2015-05-04 date_created: 2018-12-11T11:52:24Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1145/2737166.2737175 ec_funded: 1 file: - access_level: open_access checksum: c6ce681035c163a158751f240cb7d389 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:46Z date_updated: 2020-07-14T12:44:59Z file_id: '5303' file_name: IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf file_size: 467561 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 101 - 110 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_identifier: isbn: - 978-1-4503-3471-6 publication_status: published publisher: ACM publist_id: '5676' pubrep_id: '625' quality_controlled: '1' related_material: record: - id: '1155' relation: dissertation_contains status: public scopus_import: 1 status: public title: Complete composition operators for IOCO-testing theory type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1501' abstract: - lang: eng text: 'We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ' acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).' 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: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca citation: ama: Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 2015;47(2):230-264. doi:10.1007/s10703-015-0235-2 apa: Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2 chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2. ieee: K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” Formal Methods in System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015. ista: Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264. mla: Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2. short: K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264. date_created: 2018-12-11T11:52:23Z date_published: 2015-10-01T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/s10703-015-0235-2 ec_funded: 1 intvolume: ' 47' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.0835 month: '10' oa: 1 oa_version: Preprint page: 230 - 264 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '5677' quality_controlled: '1' related_material: record: - id: '1155' relation: dissertation_contains status: public scopus_import: 1 status: public title: CEGAR for compositional analysis of qualitative properties in Markov decision processes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '1602' abstract: - lang: eng text: Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks. acknowledgement: We thank anonymous reviewers for helpful comments to improve the presentation of the paper. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Prateesh full_name: Goyal, Prateesh last_name: Goyal citation: ama: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979 apa: 'Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015. https://doi.org/10.1145/2676726.2676979. ieee: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015. ista: Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109. mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109. conference: end_date: 2015-01-17 location: Mumbai, India name: 'SIGPLAN: Symposium on Principles of Programming Languages' start_date: 2015-01-15 date_created: 2018-12-11T11:52:58Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-09-07T12:01:58Z day: '01' department: - _id: KrCh doi: 10.1145/2676726.2676979 ec_funded: 1 external_id: arxiv: - '1410.7724' intvolume: ' 50' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1410.7724 month: '01' oa: 1 oa_version: Preprint page: 97 - 109 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ACM SIGPLAN Notices publication_status: published publisher: ACM publist_id: '5565' quality_controlled: '1' related_material: record: - id: '821' relation: dissertation_contains status: public scopus_import: 1 status: public title: Faster algorithms for algebraic path properties in recursive state machines with constant treewidth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2015' ... --- _id: '1604' abstract: - lang: eng text: We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551. doi:10.1145/2676726.2676968 apa: 'Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676968' chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . ACM, 2015. https://doi.org/10.1145/2676726.2676968. ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1. ACM, pp. 539–551, 2015. ista: Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551. mla: Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:10.1145/2676726.2676968. short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT 50 (2015) 539–551. conference: end_date: 2015-01-17 location: Mumbai, India name: 'SIGPLAN: Symposium on Principles of Programming Languages' start_date: 2015-01-15 date_created: 2018-12-11T11:52:59Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '01' department: - _id: KrCh doi: 10.1145/2676726.2676968 ec_funded: 1 intvolume: ' 50' issue: '1' language: - iso: eng month: '01' oa_version: None page: 539 - 551 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 'Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ' publication_identifier: isbn: - 978-1-4503-3300-9 publication_status: published publisher: ACM publist_id: '5563' pubrep_id: '523' quality_controlled: '1' related_material: record: - id: '5445' relation: earlier_version status: public - id: '821' relation: dissertation_contains status: public scopus_import: 1 status: public title: Quantitative interprocedural analysis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2015' ... --- _id: '1607' abstract: - lang: eng text: We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.' alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9' apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9. ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.' ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157.' mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157. conference: end_date: 2015-07-24 location: San Francisco, CA, USA name: 'CAV: Computer Aided Verification' start_date: 2015-07-18 date_created: 2018-12-11T11:52:59Z date_published: 2015-07-16T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '16' department: - _id: KrCh doi: 10.1007/978-3-319-21690-4_9 ec_funded: 1 intvolume: ' 9206' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.07384 month: '07' oa: 1 oa_version: Preprint page: 140 - 157 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: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '5560' quality_controlled: '1' related_material: record: - id: '5430' relation: earlier_version status: public - id: '5437' relation: earlier_version status: public - id: '821' relation: dissertation_contains status: public scopus_import: 1 status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9206 year: '2015' ... --- _id: '1714' abstract: - lang: eng text: 'We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.' 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: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Alexander full_name: Kößler, Alexander last_name: Kößler - first_name: Ulrich full_name: Schmid, Ulrich last_name: Schmid citation: ama: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9' apa: 'Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9' chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9. ieee: K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127. ista: 'Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.' mla: Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9. short: K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127. conference: end_date: 2014-12-05 location: Rome, Italy name: 'RTSS: Real-Time Systems Symposium' start_date: 2014-12-02 date_created: 2018-12-11T11:53:37Z date_published: 2015-01-15T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '15' department: - _id: KrCh doi: 10.1109/RTSS.2014.9 intvolume: ' 2015' issue: January language: - iso: eng month: '01' oa_version: None page: 118 - 127 publication: Real-Time Systems Symposium publication_status: published publisher: IEEE publist_id: '5417' quality_controlled: '1' related_material: record: - id: '5423' relation: earlier_version status: public - id: '821' relation: dissertation_contains status: public scopus_import: 1 status: public title: A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015 year: '2015' ... --- _id: '1633' abstract: - lang: eng text: "We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix." article_number: '151' author: - first_name: David full_name: Hahn, David id: 357A6A66-F248-11E8-B48F-1D18A9856A87 last_name: Hahn - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896' apa: 'Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896' chicago: Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896. ieee: 'D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.' mla: Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896. short: D. Hahn, C. Wojtan, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:09Z date_published: 2015-07-27T00:00:00Z date_updated: 2023-09-07T12:02:56Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2766896 ec_funded: 1 file: - access_level: open_access checksum: 955aee971983f6b6152bcc1c9b4a7c20 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:13Z date_updated: 2020-07-14T12:45:07Z file_id: '5131' file_name: IST-2016-609-v1+1_FractureBEM.pdf file_size: 20154270 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_status: published publisher: ACM publist_id: '5522' pubrep_id: '609' quality_controlled: '1' related_material: record: - id: '839' relation: dissertation_contains status: public scopus_import: 1 status: public title: High-resolution brittle fracture simulation with boundary elements type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1537' abstract: - lang: eng text: 3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype. acknowledged_ssus: - _id: SSU acknowledgement: 'We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ' author: - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Andrew full_name: Callan Jones, Andrew last_name: Callan Jones - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Keisuke full_name: Sako, Keisuke id: 3BED66BE-F248-11E8-B48F-1D18A9856A87 last_name: Sako orcid: 0000-0002-6453-8075 - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Monika full_name: Ritsch Marte, Monika last_name: Ritsch Marte - 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: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008 apa: Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008 chicago: Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008. ieee: V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015. ista: Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685. mla: Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008. short: V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685. date_created: 2018-12-11T11:52:35Z date_published: 2015-02-12T00:00:00Z date_updated: 2023-09-07T12:05:08Z day: '12' ddc: - '570' department: - _id: CaHe - _id: MiSi doi: 10.1016/j.cell.2015.01.008 file: - access_level: open_access checksum: 228d3edf40627d897b3875088a0ac51f content_type: application/pdf creator: system date_created: 2018-12-12T10:13:21Z date_updated: 2020-07-14T12:45:01Z file_id: '5003' file_name: IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf file_size: 4362653 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 160' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 673 - 685 project: - _id: 2529486C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T 560-B17 name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation - _id: 2527D5CC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 812-B12 name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation publication: Cell publication_status: published publisher: Cell Press publist_id: '5634' pubrep_id: '484' quality_controlled: '1' related_material: record: - id: '961' relation: dissertation_contains status: public scopus_import: 1 status: public title: Cortical contractility triggers a stochastic switch to fast amoeboid cell motility tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2015' ... --- _id: '1591' abstract: - lang: eng text: Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well. author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874' apa: 'Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874' chicago: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.' ieee: 'M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.' ista: 'Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.' mla: 'Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.' short: M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32. date_created: 2018-12-11T11:52:54Z date_published: 2015-01-20T00:00:00Z date_updated: 2023-09-07T12:06:09Z day: '20' department: - _id: JiFr doi: 10.1105/tpc.114.134874 external_id: pmid: - '25604445' intvolume: ' 27' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/ month: '01' oa: 1 oa_version: Submitted Version page: 20 - 32 pmid: 1 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5580' quality_controlled: '1' related_material: record: - id: '938' relation: dissertation_contains status: public scopus_import: 1 status: public title: 'PIN-dependent auxin transport: Action, regulation, and evolution' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1677' abstract: - lang: eng text: We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale. article_number: '103301' author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606 apa: Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4932606 chicago: Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4932606. ieee: J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” Journal of Mathematical Physics, vol. 56, no. 10. American Institute of Physics, 2015. ista: Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301. mla: Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, American Institute of Physics, 2015, doi:10.1063/1.4932606. short: J. Alt, Journal of Mathematical Physics 56 (2015). date_created: 2018-12-11T11:53:25Z date_published: 2015-10-09T00:00:00Z date_updated: 2023-09-07T12:38:08Z day: '09' department: - _id: LaEr doi: 10.1063/1.4932606 ec_funded: 1 intvolume: ' 56' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1506.04683 month: '10' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5472' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: 1 status: public title: The local semicircle law for random matrices with a fourfold symmetry type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2015' ... --- _id: '1678' abstract: - lang: eng text: High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes. acknowledgement: 'This work was supported by grants from the European Union Seventh Framework Programme (CIG-303564 to H.J. and ERC-StG-311166 to S.M.B.N.), the Human Frontier Science Program (RGY0084_2012 to H.J.) and the Herzfelder Foundation (to M.G.). A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W 1232) and a FemTech fellowship (3580812 Austrian Research Promotion Agency).' author: - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Markus full_name: Muellner, Markus last_name: Muellner - first_name: Matthias full_name: Nowak, Matthias id: 30845DAA-F248-11E8-B48F-1D18A9856A87 last_name: Nowak - first_name: Sebastian full_name: Nijman, Sebastian last_name: Nijman - first_name: Michael full_name: Grusch, Michael last_name: Grusch - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, et al. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 2015;11(12):952-954. doi:10.1038/nchembio.1933 apa: Inglés Prieto, Á., Gschaider-Reichhart, E., Muellner, M., Nowak, M., Nijman, S., Grusch, M., & Janovjak, H. L. (2015). Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.1933 chicago: Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Markus Muellner, Matthias Nowak, Sebastian Nijman, Michael Grusch, and Harald L Janovjak. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nchembio.1933. ieee: Á. Inglés Prieto et al., “Light-assisted small-molecule screening against protein kinases,” Nature Chemical Biology, vol. 11, no. 12. Nature Publishing Group, pp. 952–954, 2015. ista: Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, Nowak M, Nijman S, Grusch M, Janovjak HL. 2015. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 11(12), 952–954. mla: Inglés Prieto, Álvaro, et al. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 952–54, doi:10.1038/nchembio.1933. short: Á. Inglés Prieto, E. Gschaider-Reichhart, M. Muellner, M. Nowak, S. Nijman, M. Grusch, H.L. Janovjak, Nature Chemical Biology 11 (2015) 952–954. date_created: 2018-12-11T11:53:25Z date_published: 2015-10-12T00:00:00Z date_updated: 2023-09-07T12:49:09Z day: '12' ddc: - '571' department: - _id: HaJa - _id: LifeSc doi: 10.1038/nchembio.1933 ec_funded: 1 file: - access_level: open_access checksum: e9fb251dfcb7cd209b83f17867e61321 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:51Z date_updated: 2020-07-14T12:45:12Z file_id: '4842' file_name: IST-2017-837-v1+1_ingles-prieto.pdf file_size: 1308364 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 11' issue: '12' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 952 - 954 project: - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) - _id: 255A6082-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '5471' pubrep_id: '837' quality_controlled: '1' related_material: record: - id: '418' relation: dissertation_contains status: public scopus_import: 1 status: public title: Light-assisted small-molecule screening against protein kinases type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1576' abstract: - lang: eng text: 'Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state.' article_number: '248101' author: - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101 apa: Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101 chicago: Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101. ieee: S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015. ista: Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101. mla: Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101. short: S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015). date_created: 2018-12-11T11:52:49Z date_published: 2015-12-08T00:00:00Z date_updated: 2023-09-07T12:55:21Z day: '08' department: - _id: GaTk doi: 10.1103/PhysRevLett.115.248101 ec_funded: 1 intvolume: ' 115' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.05716 month: '12' oa: 1 oa_version: Preprint project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5595' quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: 1 status: public title: Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2015' ... --- _id: '8183' abstract: - lang: eng text: "We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample." acknowledgement: We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions. article_number: '1511.03501' article_processing_charge: No author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: A. full_name: Skopenkov, A. last_name: Skopenkov - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv. apa: Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv. chicago: Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d. ieee: S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” arXiv. . ista: Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501. mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, 1511.03501. short: S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.). date_created: 2020-07-30T10:45:19Z date_published: 2015-11-15T00:00:00Z date_updated: 2023-09-07T13:12:17Z day: '15' department: - _id: UlWa external_id: arxiv: - '1511.03501' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03501 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted related_material: record: - id: '9308' relation: later_version status: public - id: '10220' relation: later_version status: public - id: '8156' relation: dissertation_contains status: public status: public title: Eliminating higher-multiplicity intersections, III. Codimension 2 type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5441' abstract: - lang: eng text: We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks. 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: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1 apa: Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1 chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1. ieee: K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 24p. mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015, doi:10.15479/AT:IST-2015-340-v1-1. short: K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015. date_created: 2018-12-12T11:39:21Z date_published: 2015-07-11T00:00:00Z date_updated: 2023-09-19T14:36:19Z day: '11' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-340-v1-1 file: - access_level: open_access checksum: df383dc62c94d7b2ea639aba088a76c6 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:09Z date_updated: 2020-07-14T12:46:56Z file_id: '5531' file_name: IST-2015-340-v1+1_main.pdf file_size: 861396 relation: main_file file_date_updated: 2020-07-14T12:46:56Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '24' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '340' related_material: record: - id: '1437' relation: later_version status: public - id: '5442' relation: earlier_version status: public - id: '6009' relation: later_version status: public status: public title: Algorithms for algebraic path properties in concurrent systems of constant treewidth components type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...