--- _id: '9707' abstract: - lang: eng text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis. article_processing_charge: No author: - first_name: Paul full_name: Riccio, Paul last_name: Riccio - first_name: Christina full_name: Cebrián, Christina last_name: Cebrián - first_name: Hui full_name: Zong, Hui last_name: Zong - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Frank full_name: Costantini, Frank last_name: Costantini citation: ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b' apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b' chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.' ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.' ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, 10.5061/dryad.pk16b.' mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.' short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017). date_created: 2021-07-23T09:39:34Z date_published: 2017-01-14T00:00:00Z date_updated: 2022-08-25T13:34:55Z day: '14' department: - _id: SiHi doi: 10.5061/dryad.pk16b main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.pk16b month: '01' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9702' relation: used_in_publication status: deleted status: public title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9844' article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018. ieee: N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, 10.1371/journal.pgen.1007122.s018. mla: Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:27:16Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s018 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Source data for figures and tables type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '12611' abstract: - lang: eng text: 'We investigate the energy balance and ablation regimes of glaciers in high-elevation, dry environments using glaciometeorological data collected on six glaciers in the semiarid Andes of North-Central Chile (29–34°S, 3127–5324 m). We use a point-scale physically based energy balance (EB) model and an enhanced Temperature-Index (ETI) model that calculates melt rates only as a function of air temperature and net shortwave radiation. At all sites, the largest energy inputs are net shortwave and incoming longwave radiation, which are controlled by surface albedo and elevation, respectively. Turbulent fluxes cancel each other out at the lower sites, but as elevation increases, cold, dry and wind-exposed conditions increase the magnitude of negative latent heat fluxes, associated with large surface sublimation rates. In midsummer (January), ablation rates vary from 67.9 mm w.e. d−1 at the lowest site (∼100% corresponding to melt), to 2.3 mm w.e. d−1 at the highest site (>85% corresponding to surface sublimation). At low-elevation, low-albedo, melt-dominated sites, the ETI model correctly reproduces melt using a large range of possible parameters, but both the performance and parameter transferability decrease with elevation for two main reasons: (i) the air temperature threshold approach for melt onset does not capture the diurnal variability of melt in cold and strong irradiated environments and (ii) energy losses decrease the correlation between melt and net shortwave radiation. We summarize our results by means of an elevation profile of ablation components that can be used as reference in future studies of glacier ablation in the semiarid Andes.' 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: S. full_name: MacDonell, S. last_name: MacDonell - first_name: J. full_name: McPhee, J. last_name: McPhee - first_name: P. full_name: Burlando, P. last_name: Burlando citation: ama: 'Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. Water Resources Research. 2017;53(7):5601-5625. doi:10.1002/2016wr020126' apa: 'Ayala, A., Pellicciotti, F., MacDonell, S., McPhee, J., & Burlando, P. (2017). Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. Water Resources Research. American Geophysical Union. https://doi.org/10.1002/2016wr020126' chicago: 'Ayala, A., Francesca Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” Water Resources Research. American Geophysical Union, 2017. https://doi.org/10.1002/2016wr020126.' ieee: 'A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando, “Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions,” Water Resources Research, vol. 53, no. 7. American Geophysical Union, pp. 5601–5625, 2017.' ista: 'Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. 2017. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. Water Resources Research. 53(7), 5601–5625.' mla: 'Ayala, A., et al. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” Water Resources Research, vol. 53, no. 7, American Geophysical Union, 2017, pp. 5601–25, doi:10.1002/2016wr020126.' short: A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, P. Burlando, Water Resources Research 53 (2017) 5601–5625. date_created: 2023-02-20T08:14:10Z date_published: 2017-07-10T00:00:00Z date_updated: 2023-02-24T11:41:55Z day: '10' doi: 10.1002/2016wr020126 extern: '1' intvolume: ' 53' issue: '7' keyword: - Water Science and Technology language: - iso: eng month: '07' oa_version: None page: 5601-5625 publication: Water Resources Research publication_identifier: issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: 'Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2017' ... --- _id: '12612' abstract: - lang: eng text: Supraglacial ponds play a key role in absorbing atmospheric energy and directing it to the ice of debris-covered glaciers, but the spatial and temporal distribution of these features is not well documented. We analyse 172 Landsat TM/ETM+ scenes for the period 1999–2013 to identify thawed supraglacial ponds for the debris-covered tongues of five glaciers in the Langtang Valley of Nepal. We apply an advanced atmospheric correction routine (Landcor/6S) and use band ratio and image morphological techniques to identify ponds and validate our results with 2.5 m Cartosat-1 observations. We then characterize the spatial, seasonal and interannual patterns of ponds. We find high variability in pond incidence between glaciers (May–October means of 0.08–1.69% of debris area), with ponds most frequent in zones of low surface gradient and velocity. The ponds show pronounced seasonality, appearing in the pre-monsoon as snow melts, peaking at the monsoon onset at 2% of debris-covered area, then declining in the post-monsoon as ponds drain or freeze. Ponds are highly recurrent and persistent, with 40.5% of pond locations occurring for multiple years. Rather than a trend in pond cover over the study period, we find high interannual variability for each glacier after controlling for seasonality. article_processing_charge: No article_type: original author: - first_name: EVAN S. full_name: MILES, EVAN S. last_name: MILES - first_name: IAN C. full_name: WILLIS, IAN C. last_name: WILLIS - first_name: NEIL S. full_name: ARNOLD, NEIL S. last_name: ARNOLD - first_name: JAKOB full_name: STEINER, JAKOB last_name: STEINER - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. Journal of Glaciology. 2017;63(237):88-105. doi:10.1017/jog.2016.120 apa: MILES, E. S., WILLIS, I. C., ARNOLD, N. S., STEINER, J., & Pellicciotti, F. (2017). Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2016.120 chicago: MILES, EVAN S., IAN C. WILLIS, NEIL S. ARNOLD, JAKOB STEINER, and Francesca Pellicciotti. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” Journal of Glaciology. Cambridge University Press, 2017. https://doi.org/10.1017/jog.2016.120. ieee: E. S. MILES, I. C. WILLIS, N. S. ARNOLD, J. STEINER, and F. Pellicciotti, “Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013,” Journal of Glaciology, vol. 63, no. 237. Cambridge University Press, pp. 88–105, 2017. ista: MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. 2017. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. Journal of Glaciology. 63(237), 88–105. mla: MILES, EVAN S., et al. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” Journal of Glaciology, vol. 63, no. 237, Cambridge University Press, 2017, pp. 88–105, doi:10.1017/jog.2016.120. short: E.S. MILES, I.C. WILLIS, N.S. ARNOLD, J. STEINER, F. Pellicciotti, Journal of Glaciology 63 (2017) 88–105. date_created: 2023-02-20T08:14:16Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-02-24T11:38:31Z day: '01' doi: 10.1017/jog.2016.120 extern: '1' intvolume: ' 63' issue: '237' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/jog.2016.120 month: '02' oa: 1 oa_version: Published Version page: 88-105 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2017' ... --- _id: '12610' abstract: - lang: eng text: The hydrological systems of heavily-downwasted debris-covered glaciers differ from those of clean-ice glaciers due to the hummocky surface and debris mantle of such glaciers, leading to a relatively limited understanding of drainage pathways. Supraglacial ponds represent sinks within the discontinuous supraglacial drainage system, and occasionally drain englacially. To assess pond dynamics, we made pond water level measurements on Lirung Glacier, Nepal, during May and October of 2013 and 2014. Simultaneously, aerial, satellite, and terrestrial orthoimages and digital elevation models were obtained, providing snapshots of the ponds and their surroundings. We performed a DEM-based analysis of the glacier's closed surface catchments to identify surface drainage pathways and englacial drainage points, and compared this to field observations of surface and near-surface water flow. The total ponded area was higher in the pre-monsoon than post-monsoon, with individual ponds filling and draining seasonally associated with the surface exposure of englacial conduit segments. We recorded four pond drainage events, all of which occurred gradually (duration of weeks), observed diurnal fluctuations indicative of varying water supply and outflow discharge, and we documented instances of interaction between distant ponds. The DEM drainage analysis identified numerous sinks >3 m in depth across the glacier surface, few of which exhibited ponds (23%), while the field survey highlighted instances of surface water only explicable via englacial routes. Taken together, our observations provide evidence for widespread supraglacial-englacial connectivity of meltwater drainage paths. Results suggest that successive englacial conduit collapse events, themselves likely driven by supraglacial pond drainage, cause the glacier surface drainage system to evolve into a configuration following relict englacial conduit systems. Within this system, ponds form in depressions of reduced drainage efficiency and link the supraglacial and englacial drainage networks. article_number: '69' article_processing_charge: No article_type: original author: - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Jakob full_name: Steiner, Jakob last_name: Steiner - first_name: Ian full_name: Willis, Ian last_name: Willis - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel - first_name: Anna full_name: Chesnokova, Anna last_name: Chesnokova - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Miles ES, Steiner J, Willis I, et al. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. Frontiers in Earth Science. 2017;5. doi:10.3389/feart.2017.00069 apa: Miles, E. S., Steiner, J., Willis, I., Buri, P., Immerzeel, W. W., Chesnokova, A., & Pellicciotti, F. (2017). Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2017.00069 chicago: Miles, Evan S., Jakob Steiner, Ian Willis, Pascal Buri, Walter W. Immerzeel, Anna Chesnokova, and Francesca Pellicciotti. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” Frontiers in Earth Science. Frontiers Media, 2017. https://doi.org/10.3389/feart.2017.00069. ieee: E. S. Miles et al., “Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal,” Frontiers in Earth Science, vol. 5. Frontiers Media, 2017. ista: Miles ES, Steiner J, Willis I, Buri P, Immerzeel WW, Chesnokova A, Pellicciotti F. 2017. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. Frontiers in Earth Science. 5, 69. mla: Miles, Evan S., et al. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” Frontiers in Earth Science, vol. 5, 69, Frontiers Media, 2017, doi:10.3389/feart.2017.00069. short: E.S. Miles, J. Steiner, I. Willis, P. Buri, W.W. Immerzeel, A. Chesnokova, F. Pellicciotti, Frontiers in Earth Science 5 (2017). date_created: 2023-02-20T08:14:04Z date_published: 2017-09-21T00:00:00Z date_updated: 2023-02-28T11:13:23Z day: '21' doi: 10.3389/feart.2017.00069 extern: '1' intvolume: ' 5' keyword: - General Earth and Planetary Sciences language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3389/feart.2017.00069 month: '09' oa: 1 oa_version: Published Version publication: Frontiers in Earth Science publication_identifier: issn: - 2296-6463 publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2017' ... --- _id: '12609' abstract: - lang: eng text: Previous estimates of melt and surface sublimation on glaciers of the subtropical semiarid Andes (29–34°S) have been obtained at few specific locations, but it is not clear how ablation components vary across the entire extent of a glacier in this dry environment. Here, we simulate the distributed energy and mass balance of Juncal Norte Glacier (33°S) during a 2-month summer period. Forcing fields of near-surface air temperature and wind speed are generated using two methods accounting for the main physical processes that shape their spatial variations. Simulated meteorological variables and ablation agree well with observations on the glacier tongue and reveal complex patterns of energy and mass fluxes. Ablation decreases from 70 mm w.e. d−1 at the low-albedo glacier terminus (~3000 m), where almost 100% of total ablation corresponds to melt, to <5 mm w.e. d−1 at wind-exposed, strong-radiated sites above 5500 m, where surface sublimation represents >75% of total ablation. Our simulations provide the first glacier-scale estimates of ablation components on a glacier in the study region and better reproduce the observed and expected spatial variations of melt and surface sublimation, in comparison with more simple assumptions, such as linear gradients and uniform wind speeds. 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: N. full_name: PELEG, N. last_name: PELEG - first_name: P. full_name: BURLANDO, P. last_name: BURLANDO citation: ama: 'AYALA A, Pellicciotti F, PELEG N, BURLANDO P. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. Journal of Glaciology. 2017;63(241):803-822. doi:10.1017/jog.2017.46' apa: 'AYALA, A., Pellicciotti, F., PELEG, N., & BURLANDO, P. (2017). Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2017.46' chicago: 'AYALA, A., Francesca Pellicciotti, N. PELEG, and P. BURLANDO. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” Journal of Glaciology. Cambridge University Press, 2017. https://doi.org/10.1017/jog.2017.46.' ieee: 'A. AYALA, F. Pellicciotti, N. PELEG, and P. BURLANDO, “Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile,” Journal of Glaciology, vol. 63, no. 241. Cambridge University Press, pp. 803–822, 2017.' ista: 'AYALA A, Pellicciotti F, PELEG N, BURLANDO P. 2017. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. Journal of Glaciology. 63(241), 803–822.' mla: 'AYALA, A., et al. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” Journal of Glaciology, vol. 63, no. 241, Cambridge University Press, 2017, pp. 803–22, doi:10.1017/jog.2017.46.' short: A. AYALA, F. Pellicciotti, N. PELEG, P. BURLANDO, Journal of Glaciology 63 (2017) 803–822. date_created: 2023-02-20T08:13:53Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-02-28T11:28:19Z day: '01' doi: 10.1017/jog.2017.46 extern: '1' intvolume: ' 63' issue: '241' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/jog.2017.46 month: '10' oa: 1 oa_version: Published Version page: 803-822 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2017' ... --- _id: '12608' abstract: - lang: eng text: The spatio-temporal distribution of air temperature over mountain glaciers can demonstrate complex patterns, yet it is often represented simplistically using linear vertical temperature gradients (VTGs) extrapolated from off-glacier locations. We analyse a network of centreline and lateral air temperature observations at Tsanteleina Glacier, Italy, during summer 2015. On average, VTGs are steep (<−0.0065 °C m−1), but they are shallow under warm ambient conditions when the correlation between air temperature and elevation becomes weaker. Published along-flowline temperature distribution methods explain centreline observations well, including warming on the lower glacier tongue, but cannot estimate lateral temperature variability. Application of temperature distribution methods improves simulation of melt rates (RMSE) in an energy-balance model by up to 36% compared to the environmental lapse rate extrapolated from an off-glacier station. However, results suggest that model parameters are not easily transferable to glaciers with a small fetch without recalibration. Such methods have potential to improve estimates of temperature across a glacier, but their parameter transferability should be further linked to the glacier and atmospheric characteristics. Furthermore, ‘cold spots’, which can be >2°C cooler than expected for their elevation, whose occurrence is not predicted by the temperature distribution models, are identified at one-quarter of the measurement sites. article_processing_charge: No article_type: original author: - first_name: THOMAS E. full_name: SHAW, THOMAS E. last_name: SHAW - first_name: BEN W. full_name: BROCK, BEN W. last_name: BROCK - first_name: ÁLVARO full_name: AYALA, ÁLVARO last_name: AYALA - first_name: NICK full_name: RUTTER, NICK last_name: RUTTER - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: 'SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. Journal of Glaciology. 2017;63(242):973-988. doi:10.1017/jog.2017.65' apa: 'SHAW, T. E., BROCK, B. W., AYALA, Á., RUTTER, N., & Pellicciotti, F. (2017). Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2017.65' chicago: 'SHAW, THOMAS E., BEN W. BROCK, ÁLVARO AYALA, NICK RUTTER, and Francesca Pellicciotti. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” Journal of Glaciology. Cambridge University Press, 2017. https://doi.org/10.1017/jog.2017.65.' ieee: 'T. E. SHAW, B. W. BROCK, Á. AYALA, N. RUTTER, and F. Pellicciotti, “Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations,” Journal of Glaciology, vol. 63, no. 242. Cambridge University Press, pp. 973–988, 2017.' ista: 'SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. 2017. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. Journal of Glaciology. 63(242), 973–988.' mla: 'SHAW, THOMAS E., et al. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” Journal of Glaciology, vol. 63, no. 242, Cambridge University Press, 2017, pp. 973–88, doi:10.1017/jog.2017.65.' short: T.E. SHAW, B.W. BROCK, Á. AYALA, N. RUTTER, F. Pellicciotti, Journal of Glaciology 63 (2017) 973–988. date_created: 2023-02-20T08:13:47Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-02-28T11:30:34Z day: '01' doi: 10.1017/jog.2017.65 extern: '1' intvolume: ' 63' issue: '242' keyword: - Earth-Surface Processes language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/jog.2017.65 month: '12' oa: 1 oa_version: Published Version page: 973-988 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2017' ... --- _id: '12905' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss citation: ama: 'Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.' apa: 'Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing.' chicago: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017. ieee: A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28. ista: 'Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.' mla: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. short: A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. conference: end_date: 2017-03-03 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2017-03-01 date_created: 2023-05-05T12:58:53Z date_published: 2017-03-03T00:00:00Z date_updated: 2023-05-16T07:22:23Z day: '03' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: 7bcc499479d4f4c5ce6c0071c24ca6c6 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:20:50Z date_updated: 2023-05-16T07:20:50Z file_id: '12969' file_name: 2017_AHPC_Schloegl.pdf file_size: 1005486 relation: main_file success: 1 file_date_updated: 2023-05-16T07:20:50Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf month: '03' oa: 1 oa_version: Published Version page: '28' publication: AHPC17 – Austrian HPC Meeting 2017 publication_status: published publisher: FSP Scientific Computing status: public title: Scientific Computing at IST Austria type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '13160' abstract: - lang: eng text: "Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae." acknowledgement: This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Clara full_name: Waldmann, Clara last_name: Waldmann - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger citation: ama: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460. doi:10.1007/978-3-662-54577-5_26' apa: 'Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26' chicago: Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26. ieee: J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460. ista: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.' mla: Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26. short: J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2017-04-22 date_created: 2023-06-21T13:21:14Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-06-21T13:29:46Z day: '31' department: - _id: KrCh doi: 10.1007/978-3-662-54577-5_26 external_id: arxiv: - '1701.05738' intvolume: ' 10205' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1701.05738 month: '03' oa: 1 oa_version: Preprint page: 443-460 publication: Tools and Algorithms for the Construction and Analysis of Systems publication_identifier: eisbn: - '9783662545775' eissn: - 1611-3349 isbn: - '9783662545768' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Index appearance record for transforming Rabin automata into parity automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10205 year: '2017' ... --- _id: '13381' abstract: - lang: eng text: Self-assembly of inorganic nanoparticles has been used to prepare hundreds of different colloidal crystals, but almost invariably with the restriction that the particles must be densely packed. Here, we show that non–close-packed nanoparticle arrays can be fabricated through the selective removal of one of two components comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle superlattices were prepared at the liquid-air interface, including several arrangements that were previously unknown. Molecular dynamics simulations revealed the particular role of the liquid in templating the formation of superlattices not achievable through self-assembly in bulk solution. Second, upon stabilization, all of these binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous materials having the same chemical composition but differing in their nanoscale architectures. article_processing_charge: No article_type: original author: - first_name: Thumu full_name: Udayabhaskararao, Thumu last_name: Udayabhaskararao - first_name: Thomas full_name: Altantzis, Thomas last_name: Altantzis - first_name: Lothar full_name: Houben, Lothar last_name: Houben - first_name: Marc full_name: Coronado-Puchau, Marc last_name: Coronado-Puchau - first_name: Judith full_name: Langer, Judith last_name: Langer - first_name: Ronit full_name: Popovitz-Biro, Ronit last_name: Popovitz-Biro - first_name: Luis M. full_name: Liz-Marzán, Luis M. last_name: Liz-Marzán - first_name: Lela full_name: Vuković, Lela last_name: Vuković - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Sara full_name: Bals, Sara last_name: Bals - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Udayabhaskararao T, Altantzis T, Houben L, et al. Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. Science. 2017;358(6362):514-518. doi:10.1126/science.aan6046 apa: Udayabhaskararao, T., Altantzis, T., Houben, L., Coronado-Puchau, M., Langer, J., Popovitz-Biro, R., … Klajn, R. (2017). Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aan6046 chicago: Udayabhaskararao, Thumu, Thomas Altantzis, Lothar Houben, Marc Coronado-Puchau, Judith Langer, Ronit Popovitz-Biro, Luis M. Liz-Marzán, et al. “Tunable Porous Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aan6046. ieee: T. Udayabhaskararao et al., “Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices,” Science, vol. 358, no. 6362. American Association for the Advancement of Science, pp. 514–518, 2017. ista: Udayabhaskararao T, Altantzis T, Houben L, Coronado-Puchau M, Langer J, Popovitz-Biro R, Liz-Marzán LM, Vuković L, Král P, Bals S, Klajn R. 2017. Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices. Science. 358(6362), 514–518. mla: Udayabhaskararao, Thumu, et al. “Tunable Porous Nanoallotropes Prepared by Post-Assembly Etching of Binary Nanoparticle Superlattices.” Science, vol. 358, no. 6362, American Association for the Advancement of Science, 2017, pp. 514–18, doi:10.1126/science.aan6046. short: T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer, R. Popovitz-Biro, L.M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Science 358 (2017) 514–518. date_created: 2023-08-01T09:41:16Z date_published: 2017-10-27T00:00:00Z date_updated: 2023-08-07T11:25:00Z day: '27' doi: 10.1126/science.aan6046 extern: '1' external_id: pmid: - '29074773' intvolume: ' 358' issue: '6362' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://repository.uantwerpen.be/docman/irua/8d722e/147242_2018_06_07.pdf month: '10' oa: 1 oa_version: Submitted Version page: 514-518 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: Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 358 year: '2017' ... --- _id: '13380' abstract: - lang: eng text: Although dissipative self-assembly is ubiquitous in nature, where it gives rise to structures and functions critical to life, examples of artificial systems featuring this mode of self-assembly are rare. Here, we identify the presence of ephemeral assemblies during seeded growth of gold nanoparticles. In this process, hydrazine reduces Au(III) ions, which attach to the existing nanoparticles “seeds”. The attachment is accompanied by a local increase in the concentration of a surfactant, which therefore forms a bilayer on nanoparticle surfaces, inducing their assembly. The resulting aggregates gradually disassemble as the surfactant concentration throughout the solution equilibrates. The lifetimes of the out-of-equilibrium aggregates depend on and can be controlled by the size of the constituent nanoparticles. We demonstrate the utility of our out-of-equilibrium aggregates to form transient reflective coatings on polar surfaces. article_processing_charge: No article_type: original author: - first_name: Michał full_name: Sawczyk, Michał last_name: Sawczyk - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Sawczyk M, Klajn R. Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles. Journal of the American Chemical Society. 2017;139(49):17973-17978. doi:10.1021/jacs.7b09111 apa: Sawczyk, M., & Klajn, R. (2017). Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.7b09111 chicago: Sawczyk, Michał, and Rafal Klajn. “Out-of-Equilibrium Aggregates and Coatings during Seeded Growth of Metallic Nanoparticles.” Journal of the American Chemical Society. American Chemical Society, 2017. https://doi.org/10.1021/jacs.7b09111. ieee: M. Sawczyk and R. Klajn, “Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles,” Journal of the American Chemical Society, vol. 139, no. 49. American Chemical Society, pp. 17973–17978, 2017. ista: Sawczyk M, Klajn R. 2017. Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles. Journal of the American Chemical Society. 139(49), 17973–17978. mla: Sawczyk, Michał, and Rafal Klajn. “Out-of-Equilibrium Aggregates and Coatings during Seeded Growth of Metallic Nanoparticles.” Journal of the American Chemical Society, vol. 139, no. 49, American Chemical Society, 2017, pp. 17973–78, doi:10.1021/jacs.7b09111. short: M. Sawczyk, R. Klajn, Journal of the American Chemical Society 139 (2017) 17973–17978. date_created: 2023-08-01T09:41:01Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-08-07T11:19:30Z day: '01' doi: 10.1021/jacs.7b09111 extern: '1' external_id: pmid: - '29193964' intvolume: ' 139' issue: '49' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '12' oa_version: None page: 17973-17978 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Out-of-equilibrium aggregates and coatings during seeded growth of metallic nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 139 year: '2017' ... --- _id: '13383' abstract: - lang: eng text: Two novel donor–acceptor Stenhouse adducts (DASAs) featuring the catechol moiety were synthesized and characterized. Both compounds bind strongly to the surfaces of magnetite nanoparticles. An adrenaline-derived DASA renders the particles insoluble in all common solvents, likely because of poor solvation of the zwitterionic isomer generated on the nanoparticle surfaces. Well-soluble nanoparticles were successfully obtained using dopamine-derived DASA equipped with a long alkyl chain. Upon its attachment to nanoparticles, this DASA undergoes an irreversible decoloration reaction owing to the formation of the zwitterionic form. The reaction follows first-order kinetics and proceeds more rapidly on large nanoparticles. Interestingly, decoloration can be suppressed in the presence of free DASA molecules in solution or at high nanoparticle concentrations. article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Ahrens, Johannes last_name: Ahrens - first_name: Tong full_name: Bian, Tong last_name: Bian - first_name: Tom full_name: Vexler, Tom last_name: Vexler - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Ahrens J, Bian T, Vexler T, Klajn R. Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles. ChemPhotoChem. 2017;1(5):230-236. doi:10.1002/cptc.201700009 apa: Ahrens, J., Bian, T., Vexler, T., & Klajn, R. (2017). Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles. ChemPhotoChem. Wiley. https://doi.org/10.1002/cptc.201700009 chicago: Ahrens, Johannes, Tong Bian, Tom Vexler, and Rafal Klajn. “Irreversible Bleaching of Donor-Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles.” ChemPhotoChem. Wiley, 2017. https://doi.org/10.1002/cptc.201700009. ieee: J. Ahrens, T. Bian, T. Vexler, and R. Klajn, “Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles,” ChemPhotoChem, vol. 1, no. 5. Wiley, pp. 230–236, 2017. ista: Ahrens J, Bian T, Vexler T, Klajn R. 2017. Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles. ChemPhotoChem. 1(5), 230–236. mla: Ahrens, Johannes, et al. “Irreversible Bleaching of Donor-Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles.” ChemPhotoChem, vol. 1, no. 5, Wiley, 2017, pp. 230–36, doi:10.1002/cptc.201700009. short: J. Ahrens, T. Bian, T. Vexler, R. Klajn, ChemPhotoChem 1 (2017) 230–236. date_created: 2023-08-01T09:41:43Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-08-07T12:08:05Z day: '01' doi: 10.1002/cptc.201700009 extern: '1' intvolume: ' 1' issue: '5' keyword: - Organic Chemistry - Physical and Theoretical Chemistry - Analytical Chemistry language: - iso: eng month: '05' oa_version: None page: 230-236 publication: ChemPhotoChem publication_identifier: eissn: - 2367-0932 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Irreversible bleaching of donor-acceptor stenhouse adducts on the surfaces of magnetite nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2017' ... --- _id: '13384' abstract: - lang: eng text: Although methane is a volatile gas, it can be efficiently trapped in ice, which can then be readily set on fire. Beyond the curiosity of this “burning ice,” caged methane is of great importance as one of the world's largest natural gas resources. In these materials, known as clathrates, methane molecules are tightly bound in nanometer-sized, regularly interspaced cages. Other inorganic materials, such as the silica mineral chibaite, can similarly encapsulate methane and higher hydrocarbons. Simple organic compounds have also been found to trap various organic molecules upon crystallization. article_processing_charge: No article_type: original author: - first_name: Dipak full_name: Samanta, Dipak last_name: Samanta - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Samanta D, Klajn R. Clathrates grow up. Science. 2017;355(6328):912-912. doi:10.1126/science.aam7927 apa: Samanta, D., & Klajn, R. (2017). Clathrates grow up. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam7927 chicago: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam7927. ieee: D. Samanta and R. Klajn, “Clathrates grow up,” Science, vol. 355, no. 6328. American Association for the Advancement of Science, pp. 912–912, 2017. ista: Samanta D, Klajn R. 2017. Clathrates grow up. Science. 355(6328), 912–912. mla: Samanta, Dipak, and Rafal Klajn. “Clathrates Grow Up.” Science, vol. 355, no. 6328, American Association for the Advancement of Science, 2017, pp. 912–912, doi:10.1126/science.aam7927. short: D. Samanta, R. Klajn, Science 355 (2017) 912–912. date_created: 2023-08-01T09:41:55Z date_published: 2017-03-03T00:00:00Z date_updated: 2023-08-07T12:23:03Z day: '03' doi: 10.1126/science.aam7927 extern: '1' external_id: pmid: - '28254902' intvolume: ' 355' issue: '6328' keyword: - Multidisciplinary language: - iso: eng month: '03' oa_version: None page: 912-912 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: Clathrates grow up type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 355 year: '2017' ... --- _id: '13382' article_processing_charge: No article_type: letter_note author: - first_name: Jan H. full_name: van Esch, Jan H. last_name: van Esch - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Sijbren full_name: Otto, Sijbren last_name: Otto citation: ama: van Esch JH, Klajn R, Otto S. Chemical systems out of equilibrium. Chemical Society Reviews. 2017;46(18):5474-5475. doi:10.1039/c7cs90088k apa: van Esch, J. H., Klajn, R., & Otto, S. (2017). Chemical systems out of equilibrium. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c7cs90088k chicago: Esch, Jan H. van, Rafal Klajn, and Sijbren Otto. “Chemical Systems out of Equilibrium.” Chemical Society Reviews. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7cs90088k. ieee: J. H. van Esch, R. Klajn, and S. Otto, “Chemical systems out of equilibrium,” Chemical Society Reviews, vol. 46, no. 18. Royal Society of Chemistry, pp. 5474–5475, 2017. ista: van Esch JH, Klajn R, Otto S. 2017. Chemical systems out of equilibrium. Chemical Society Reviews. 46(18), 5474–5475. mla: van Esch, Jan H., et al. “Chemical Systems out of Equilibrium.” Chemical Society Reviews, vol. 46, no. 18, Royal Society of Chemistry, 2017, pp. 5474–75, doi:10.1039/c7cs90088k. short: J.H. van Esch, R. Klajn, S. Otto, Chemical Society Reviews 46 (2017) 5474–5475. date_created: 2023-08-01T09:41:30Z date_published: 2017-09-08T00:00:00Z date_updated: 2023-08-07T11:27:42Z day: '08' doi: 10.1039/c7cs90088k extern: '1' external_id: pmid: - '28884760' intvolume: ' 46' issue: '18' keyword: - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/c7cs90088k month: '09' oa: 1 oa_version: Published Version page: 5474-5475 pmid: 1 publication: Chemical Society Reviews publication_identifier: eissn: - 1460-4744 issn: - 0306-0012 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Chemical systems out of equilibrium type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2017' ... --- _id: '13477' abstract: - lang: eng text: Most massive stars, the progenitors of core-collapse supernovae, are in close binary systems and may interact with their companion through mass transfer or merging. We undertake a population synthesis study to compute the delay-time distribution of core-collapse supernovae, that is, the supernova rate versus time following a starburst, taking into account binary interactions. We test the systematic robustness of our results by running various simulations to account for the uncertainties in our standard assumptions. We find that a significant fraction, 15+9-8%, of core-collapse supernovae are “late”, that is, they occur 50–200 Myr after birth, when all massive single stars have already exploded. These late events originate predominantly from binary systems with at least one, or, in most cases, with both stars initially being of intermediate mass (4–8 M⊙). The main evolutionary channels that contribute often involve either the merging of the initially more massive primary star with its companion or the engulfment of the remaining core of the primary by the expanding secondary that has accreted mass at an earlier evolutionary stage. Also, the total number of core-collapse supernovae increases by 14+15-14% because of binarity for the same initial stellar mass. The high rate implies that we should have already observed such late core-collapse supernovae, but have not recognized them as such. We argue that φ Persei is a likely progenitor and that eccentric neutron star – white dwarf systems are likely descendants. Late events can help explain the discrepancy in the delay-time distributions derived from supernova remnants in the Magellanic Clouds and extragalactic type Ia events, lowering the contribution of prompt Ia events. We discuss ways to test these predictions and speculate on the implications for supernova feedback in simulations of galaxy evolution. article_number: A29 article_processing_charge: No article_type: original author: - first_name: E. full_name: Zapartas, E. last_name: Zapartas - first_name: S. E. full_name: de Mink, S. E. last_name: de Mink - first_name: R. G. full_name: Izzard, R. G. last_name: Izzard - first_name: S.-C. full_name: Yoon, S.-C. last_name: Yoon - first_name: C. full_name: Badenes, C. last_name: Badenes - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: A. full_name: de Koter, A. last_name: de Koter - first_name: C. J. full_name: Neijssel, C. J. last_name: Neijssel - first_name: M. full_name: Renzo, M. last_name: Renzo - first_name: A. full_name: Schootemeijer, A. last_name: Schootemeijer - first_name: T. S. full_name: Shrotriya, T. S. last_name: Shrotriya citation: ama: Zapartas E, de Mink SE, Izzard RG, et al. Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. 2017;601(A&A). doi:10.1051/0004-6361/201629685 apa: Zapartas, E., de Mink, S. E., Izzard, R. G., Yoon, S.-C., Badenes, C., Götberg, Y. L. L., … Shrotriya, T. S. (2017). Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201629685 chicago: Zapartas, E., S. E. de Mink, R. G. Izzard, S.-C. Yoon, C. Badenes, Ylva Louise Linsdotter Götberg, A. de Koter, et al. “Delay-Time Distribution of Core-Collapse Supernovae with Late Events Resulting from Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2017. https://doi.org/10.1051/0004-6361/201629685. ieee: E. Zapartas et al., “Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction,” Astronomy & Astrophysics, vol. 601, no. A&A. EDP Sciences, 2017. ista: Zapartas E, de Mink SE, Izzard RG, Yoon S-C, Badenes C, Götberg YLL, de Koter A, Neijssel CJ, Renzo M, Schootemeijer A, Shrotriya TS. 2017. Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. 601(A&A), A29. mla: Zapartas, E., et al. “Delay-Time Distribution of Core-Collapse Supernovae with Late Events Resulting from Binary Interaction.” Astronomy & Astrophysics, vol. 601, no. A&A, A29, EDP Sciences, 2017, doi:10.1051/0004-6361/201629685. short: E. Zapartas, S.E. de Mink, R.G. Izzard, S.-C. Yoon, C. Badenes, Y.L.L. Götberg, A. de Koter, C.J. Neijssel, M. Renzo, A. Schootemeijer, T.S. Shrotriya, Astronomy & Astrophysics 601 (2017). date_created: 2023-08-03T10:15:18Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-08-09T11:15:49Z day: '01' doi: 10.1051/0004-6361/201629685 extern: '1' external_id: arxiv: - '1701.07032' intvolume: ' 601' issue: A&A keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201629685 month: '05' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 601 year: '2017' ... --- _id: '13476' abstract: - lang: eng text: Understanding ionizing fluxes of stellar populations is crucial for various astrophysical problems including the epoch of reionization. Short-lived massive stars are generally considered as the main stellar sources. We examine the potential role of less massive stars that lose their envelope through interaction with a binary companion. Here, we focus on the role of metallicity (Z). For this purpose we used the evolutionary code MESA and created tailored atmosphere models with the radiative transfer code CMFGEN. We show that typical progenitors, with initial masses of 12 M⊙, produce hot and compact stars (~ 4 M⊙, 60–80 kK, ~1 R⊙). These stripped stars copiously produce ionizing photons, emitting 60–85% and 30–60% of their energy as HI and HeI ionizing radiation, for Z = 0.0001–0.02, respectively. Their output is comparable to what massive stars emit during their Wolf-Rayet phase, if we account for their longer lifetimes and the favorable slope of the initial mass function. Their relative importance for reionization may be further favored since they emit their photons with a time delay (~ 20 Myr after birth in our fiducial model). This allows time for the dispersal of the birth clouds, allowing the ionizing photons to escape into the intergalactic medium. At low Z, we find that Roche stripping fails to fully remove the H-rich envelope, because of the reduced opacity in the subsurface layers. This is in sharp contrast with the assumption of complete stripping that is made in rapid population synthesis simulations, which are widely used to simulate the binary progenitors of supernovae and gravitational waves. Finally, we discuss the urgency to increase the observed sample of stripped stars to test these models and we discuss how our predictions can help to design efficient observational campaigns. article_number: A11 article_processing_charge: No article_type: original author: - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: S. E. full_name: de Mink, S. E. last_name: de Mink - first_name: J. H. full_name: Groh, J. H. last_name: Groh citation: ama: 'Götberg YLL, de Mink SE, Groh JH. Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. 2017;608. doi:10.1051/0004-6361/201730472' apa: 'Götberg, Y. L. L., de Mink, S. E., & Groh, J. H. (2017). Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201730472' chicago: 'Götberg, Ylva Louise Linsdotter, S. E. de Mink, and J. H. Groh. “Ionizing Spectra of Stars That Lose Their Envelope through Interaction with a Binary Companion: Role of Metallicity.” Astronomy & Astrophysics. EDP Sciences, 2017. https://doi.org/10.1051/0004-6361/201730472.' ieee: 'Y. L. L. Götberg, S. E. de Mink, and J. H. Groh, “Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity,” Astronomy & Astrophysics, vol. 608. EDP Sciences, 2017.' ista: 'Götberg YLL, de Mink SE, Groh JH. 2017. Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. 608, A11.' mla: 'Götberg, Ylva Louise Linsdotter, et al. “Ionizing Spectra of Stars That Lose Their Envelope through Interaction with a Binary Companion: Role of Metallicity.” Astronomy & Astrophysics, vol. 608, A11, EDP Sciences, 2017, doi:10.1051/0004-6361/201730472.' short: Y.L.L. Götberg, S.E. de Mink, J.H. Groh, Astronomy & Astrophysics 608 (2017). date_created: 2023-08-03T10:15:09Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-08-09T11:27:06Z day: '01' doi: 10.1051/0004-6361/201730472 extern: '1' external_id: arxiv: - '1701.07439' intvolume: ' 608' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201730472 month: '12' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 608 year: '2017' ... --- _id: '14031' abstract: - lang: eng text: High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy. article_number: '203201' article_processing_charge: No article_type: original author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Simon full_name: Brennecke, Simon last_name: Brennecke - first_name: Manfred full_name: Lein, Manfred last_name: Lein - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20). doi:10.1103/physrevlett.119.203201 apa: Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201 chicago: Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/physrevlett.119.203201. ieee: D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” Physical Review Letters, vol. 119, no. 20. American Physical Society, 2017. ista: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201. mla: Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201. short: D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017). date_created: 2023-08-10T06:48:12Z date_published: 2017-11-17T00:00:00Z date_updated: 2023-08-22T06:48:28Z day: '17' doi: 10.1103/physrevlett.119.203201 extern: '1' external_id: arxiv: - '1710.04474' pmid: - '29219334' intvolume: ' 119' issue: '20' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.04474 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Signatures of electronic structure in bicircular high-harmonic spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '14004' abstract: - lang: eng text: High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy. article_number: '203201' article_processing_charge: No article_type: original author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Simon full_name: Brennecke, Simon last_name: Brennecke - first_name: Manfred full_name: Lein, Manfred last_name: Lein - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20). doi:10.1103/physrevlett.119.203201 apa: Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201 chicago: Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/physrevlett.119.203201. ieee: D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” Physical Review Letters, vol. 119, no. 20. American Physical Society, 2017. ista: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201. mla: Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201. short: D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017). date_created: 2023-08-10T06:35:51Z date_published: 2017-11-17T00:00:00Z date_updated: 2023-08-22T08:21:10Z day: '17' doi: 10.1103/physrevlett.119.203201 extern: '1' external_id: arxiv: - '1710.04474' intvolume: ' 119' issue: '20' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.04474 month: '11' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Signatures of electronic structure in bicircular high-harmonic spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '14005' abstract: - lang: eng text: Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales. article_number: '15651' article_processing_charge: No article_type: original author: - first_name: Samuel G. full_name: Walt, Samuel G. last_name: Walt - first_name: Niraghatam full_name: Bhargava Ram, Niraghatam last_name: Bhargava Ram - first_name: Marcos full_name: Atala, Marcos last_name: Atala - first_name: Nikolay I full_name: Shvetsov-Shilovski, Nikolay I last_name: Shvetsov-Shilovski - 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: Manfred full_name: Lein, Manfred last_name: Lein - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. 2017;8. doi:10.1038/ncomms15651 apa: Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta, A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms15651 chicago: Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski, Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651. ieee: S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering,” Nature Communications, vol. 8. Springer Nature, 2017. ista: Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. 8, 15651. mla: Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” Nature Communications, vol. 8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651. short: S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta, D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017). date_created: 2023-08-10T06:36:09Z date_published: 2017-06-15T00:00:00Z date_updated: 2023-08-22T08:26:06Z day: '15' doi: 10.1038/ncomms15651 extern: '1' external_id: pmid: - '28643771' intvolume: ' 8' 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/ncomms15651 month: '06' 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: Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '14008' abstract: - lang: eng text: Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically been limited to large-scale facilities, to subpicosecond temporal resolution, and to the condensed phase. We report the realization of TR-XAS with a temporal resolution in the low femtosecond range by developing a tabletop high-harmonic source reaching up to 350 electron volts, thus partially covering the spectral region of 280 to 530 electron volts, where water is transmissive. We used this source to follow previously unexamined light-induced chemical reactions in the lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase. By probing element-specific core-to-valence transitions at the carbon K-edge or the sulfur L-edges, we characterized their reaction paths and observed the effect of symmetry breaking through the splitting of absorption bands and Rydberg-valence mixing induced by the geometry changes. article_processing_charge: No article_type: original author: - first_name: Yoann full_name: Pertot, Yoann last_name: Pertot - first_name: Cédric full_name: Schmidt, Cédric last_name: Schmidt - first_name: Mary full_name: Matthews, Mary last_name: Matthews - first_name: Adrien full_name: Chauvet, Adrien last_name: Chauvet - first_name: Martin full_name: Huppert, Martin last_name: Huppert - first_name: Vit full_name: Svoboda, Vit last_name: Svoboda - first_name: Aaron full_name: von Conta, Aaron last_name: von Conta - first_name: Andres full_name: Tehlar, Andres last_name: Tehlar - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Jean-Pierre full_name: Wolf, Jean-Pierre last_name: Wolf - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. Science. 2017;355(6322):264-267. doi:10.1126/science.aah6114 apa: Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V., … Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aah6114 chicago: Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert, Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water Window High-Harmonic Source.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aah6114. ieee: Y. Pertot et al., “Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source,” Science, vol. 355, no. 6322. American Association for the Advancement of Science, pp. 264–267, 2017. ista: Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267. mla: Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water Window High-Harmonic Source.” Science, vol. 355, no. 6322, American Association for the Advancement of Science, 2017, pp. 264–67, doi:10.1126/science.aah6114. short: Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A. von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017) 264–267. date_created: 2023-08-10T06:36:39Z date_published: 2017-01-05T00:00:00Z date_updated: 2023-08-22T08:34:38Z day: '05' doi: 10.1126/science.aah6114 extern: '1' external_id: pmid: - '28059713' intvolume: ' 355' issue: '6322' keyword: - Multidisciplinary language: - iso: eng month: '01' oa_version: None page: 264-267 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: Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 355 year: '2017' ... --- _id: '14006' abstract: - lang: eng text: We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N2O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H2O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology. article_number: '124306' article_processing_charge: No article_type: original author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Wörner HJ. Theory of attosecond delays in molecular photoionization. The Journal of Chemical Physics. 2017;146(12). doi:10.1063/1.4977933 apa: Baykusheva, D. R., & Wörner, H. J. (2017). Theory of attosecond delays in molecular photoionization. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4977933 chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4977933. ieee: D. R. Baykusheva and H. J. Wörner, “Theory of attosecond delays in molecular photoionization,” The Journal of Chemical Physics, vol. 146, no. 12. AIP Publishing, 2017. ista: Baykusheva DR, Wörner HJ. 2017. Theory of attosecond delays in molecular photoionization. The Journal of Chemical Physics. 146(12), 124306. mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” The Journal of Chemical Physics, vol. 146, no. 12, 124306, AIP Publishing, 2017, doi:10.1063/1.4977933. short: D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (2017). date_created: 2023-08-10T06:36:19Z date_published: 2017-03-28T00:00:00Z date_updated: 2023-08-22T08:30:59Z day: '28' doi: 10.1063/1.4977933 extern: '1' external_id: pmid: - '28388142' intvolume: ' 146' issue: '12' keyword: - Physical and Theoretical Chemistry - General Physics and Astronomy language: - iso: eng month: '03' oa_version: None pmid: 1 publication: The Journal of Chemical Physics publication_identifier: eissn: - 1089-7690 issn: - 0021-9606 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Theory of attosecond delays in molecular photoionization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2017' ... --- _id: '14009' abstract: - lang: eng text: Attosecond delays between photoelectron wave packets emitted from different electronic shells are now well established. Is there any delay between electrons originating from the same electronic shell but leaving the cation in different fine-structure states? This question is relevant for all attosecond photoemission studies involving heavy elements, be it atoms, molecules or solids. We answer this fundamental question by measuring energy-dependent delays between photoelectron wave packets associated with the 2P3/2 and 2P1/2 components of the electronic groundstates of Xe+ and Kr+. We observe delays reaching up to 33±6 as in the case of Xe. Our results are compared with two state-of-the-art theories. Whereas both theories quantitatively agree with the results obtained for Kr, neither of them fully reproduces the experimental results in Xe. Performing delay measurements very close to the ionization thresholds, we compare the agreement of several analytical formulas for the continuum-continuum delays with experimental data. Our results show an important influence of spin-orbit coupling on attosecond photoionization delays, highlight the requirement for additional theory development, and offer a precision benchmark for such work. article_number: '013404' article_processing_charge: No article_type: original author: - first_name: I. full_name: Jordan, I. last_name: Jordan - first_name: M. full_name: Huppert, M. last_name: Huppert - first_name: S. full_name: Pabst, S. last_name: Pabst - first_name: A. S. full_name: Kheifets, A. S. last_name: Kheifets - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: H. J. full_name: Wörner, H. J. last_name: Wörner citation: ama: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. Spin-orbit delays in photoemission. Physical Review A. 2017;95(1). doi:10.1103/physreva.95.013404 apa: Jordan, I., Huppert, M., Pabst, S., Kheifets, A. S., Baykusheva, D. R., & Wörner, H. J. (2017). Spin-orbit delays in photoemission. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.95.013404 chicago: Jordan, I., M. Huppert, S. Pabst, A. S. Kheifets, Denitsa Rangelova Baykusheva, and H. J. Wörner. “Spin-Orbit Delays in Photoemission.” Physical Review A. American Physical Society, 2017. https://doi.org/10.1103/physreva.95.013404. ieee: I. Jordan, M. Huppert, S. Pabst, A. S. Kheifets, D. R. Baykusheva, and H. J. Wörner, “Spin-orbit delays in photoemission,” Physical Review A, vol. 95, no. 1. American Physical Society, 2017. ista: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. 2017. Spin-orbit delays in photoemission. Physical Review A. 95(1), 013404. mla: Jordan, I., et al. “Spin-Orbit Delays in Photoemission.” Physical Review A, vol. 95, no. 1, 013404, American Physical Society, 2017, doi:10.1103/physreva.95.013404. short: I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner, Physical Review A 95 (2017). date_created: 2023-08-10T06:36:58Z date_published: 2017-01-10T00:00:00Z date_updated: 2023-08-22T08:38:17Z day: '10' doi: 10.1103/physreva.95.013404 extern: '1' intvolume: ' 95' issue: '1' language: - iso: eng month: '01' oa_version: None publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Spin-orbit delays in photoemission type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2017' ... --- _id: '14007' abstract: - lang: eng text: 'In a recent article by Hockett et al (2016 J. Phys. B: At. Mol. Opt. Phys. 49 095602), time delays arising in the context of molecular single-photon ionization are investigated from a theoretical point of view. We argue that one of the central equations given in this article is incorrect and present a reformulation that is consistent with the established treatment of angle-dependent scattering delays (Eisenbud 1948 PhD Thesis Princeton University; Wigner 1955 Phys. Rev. 98 145–7; Smith 1960 Phys. Rev. 118 349–6; Nussenzveig 1972 Phys. Rev. D 6 1534–42).' article_number: '078002' article_processing_charge: No article_type: letter_note author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: 'Baykusheva DR, Wörner HJ. Comment on ‘Time delays in molecular photoionization.’ Journal of Physics B: Atomic, Molecular and Optical Physics. 2017;50(7). doi:10.1088/1361-6455/aa62b5' apa: 'Baykusheva, D. R., & Wörner, H. J. (2017). Comment on ‘Time delays in molecular photoionization.’ Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/aa62b5' chicago: 'Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2017. https://doi.org/10.1088/1361-6455/aa62b5.' ieee: 'D. R. Baykusheva and H. J. Wörner, “Comment on ‘Time delays in molecular photoionization,’” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 50, no. 7. IOP Publishing, 2017.' ista: 'Baykusheva DR, Wörner HJ. 2017. Comment on ‘Time delays in molecular photoionization’. Journal of Physics B: Atomic, Molecular and Optical Physics. 50(7), 078002.' mla: 'Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 50, no. 7, 078002, IOP Publishing, 2017, doi:10.1088/1361-6455/aa62b5.' short: 'D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 50 (2017).' date_created: 2023-08-10T06:36:29Z date_published: 2017-03-15T00:00:00Z date_updated: 2023-08-22T08:32:43Z day: '15' doi: 10.1088/1361-6455/aa62b5 extern: '1' external_id: arxiv: - '1611.09352' intvolume: ' 50' issue: '7' keyword: - Condensed Matter Physics - Atomic and Molecular Physics - and Optics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.09352 month: '03' oa: 1 oa_version: Preprint publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_identifier: eissn: - 1361-6455 issn: - 0953-4075 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Comment on ‘Time delays in molecular photoionization’ type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2017' ... --- _id: '950' abstract: - lang: eng text: "Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n" alternative_title: - LIPIcs article_number: '17' author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - 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: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev citation: ama: 'Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21' apa: 'Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21' chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21. ieee: 'G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.' ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.' mla: Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21. short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'CONCUR: Concurrency Theory' start_date: 2017-09-05 date_created: 2018-12-11T11:49:22Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-08-29T07:02:13Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2017.21 external_id: arxiv: - '1705.01433' file: - access_level: open_access checksum: 6d5cccf755207b91ccbef95d8275b013 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:00Z date_updated: 2020-07-14T12:48:16Z file_id: '5318' file_name: IST-2017-844-v1+1_concur-cr.pdf file_size: 335170 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 85' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6466' pubrep_id: '844' quality_controlled: '1' related_material: record: - id: '6752' relation: later_version status: public scopus_import: 1 status: public title: Infinite-duration bidding games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2017' ... --- _id: '683' abstract: - lang: eng text: 'Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.' alternative_title: - LIPIcs article_number: '49' author: - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49' apa: 'Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49' chicago: Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49. ieee: 'A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.' ista: 'Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.' mla: Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.SoCG.2017.49. short: A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-07-07 location: Brisbane, Australia name: 'SoCG: Symposium on Computational Geometry' start_date: 2017-07-04 date_created: 2018-12-11T11:47:54Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-05T15:01:43Z day: '01' ddc: - '514' - '516' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2017.49 file: - access_level: open_access checksum: 24fdde981cc513352a78dcf9b0660ae9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:12Z date_updated: 2020-07-14T12:47:41Z file_id: '5265' file_name: IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf file_size: 710007 relation: main_file file_date_updated: 2020-07-14T12:47:41Z has_accepted_license: '1' intvolume: ' 77' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7033' pubrep_id: '896' quality_controlled: '1' related_material: record: - id: '5986' relation: later_version status: public scopus_import: 1 status: public title: A proof of the orbit conjecture for flipping edge labelled triangulations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '1155' abstract: - lang: eng text: This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results. acknowledgement: ' First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca citation: ama: Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730 apa: Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730 chicago: Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730. ieee: P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017. ista: Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria. mla: Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730. short: P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:50:27Z date_published: 2017-01-02T00:00:00Z date_updated: 2023-09-07T11:58:34Z day: '02' ddc: - '004' - '005' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:TH_730 ec_funded: 1 file: - access_level: open_access checksum: 1406a681cb737508234fde34766be2c2 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:26Z date_updated: 2020-07-14T12:44:34Z file_id: '4880' file_name: IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf file_size: 1028586 relation: main_file file_date_updated: 2020-07-14T12:44:34Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '163' project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6203' pubrep_id: '730' related_material: record: - id: '1093' relation: part_of_dissertation status: public - id: '1230' relation: part_of_dissertation status: public - id: '1234' relation: part_of_dissertation status: public - id: '1391' relation: part_of_dissertation status: public - id: '1501' relation: part_of_dissertation status: public - id: '1502' relation: part_of_dissertation status: public - id: '2063' relation: part_of_dissertation status: public - id: '2167' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 title: Statistical and logical methods for property checking type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6291' abstract: - lang: eng text: Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pavel full_name: Payne, Pavel id: 35F78294-F248-11E8-B48F-1D18A9856A87 last_name: Payne orcid: 0000-0002-2711-9453 citation: ama: Payne P. Bacterial herd and social immunity to phages. 2017. apa: Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria. chicago: Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017. ieee: P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017. ista: Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria. mla: Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017. short: P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017. date_created: 2019-04-09T15:16:45Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-07T12:00:00Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: NiBa - _id: JoBo file: - access_level: closed checksum: a0fc5c26a89c0ea759947ffba87d0d8f content_type: application/pdf creator: dernst date_created: 2019-04-09T15:15:32Z date_updated: 2020-07-14T12:47:27Z file_id: '6292' file_name: thesis_pavel_payne_final_w_signature_page.pdf file_size: 3025175 relation: main_file - access_level: open_access checksum: af531e921a7f64a9e0af4cd8783b2226 content_type: application/pdf creator: dernst date_created: 2021-02-22T13:45:59Z date_updated: 2021-02-22T13:45:59Z file_id: '9187' file_name: 2017_Payne_Thesis.pdf file_size: 3111536 relation: main_file success: 1 file_date_updated: 2021-02-22T13:45:59Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '83' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Bacterial herd and social immunity to phages type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '561' abstract: - lang: eng text: Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape. acknowledgement: This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. article_number: '20170646' article_processing_charge: No article_type: original author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646 apa: Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646 chicago: Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646. ieee: M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017. ista: Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646. mla: Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646. short: M. Pleska, C.C. Guet, Biology Letters 13 (2017). date_created: 2018-12-11T11:47:11Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-07T11:59:32Z day: '01' department: - _id: CaGu doi: 10.1098/rsbl.2017.0646 external_id: pmid: - '29237814' intvolume: ' 13' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rsbl.2017.0646 month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant) - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication: Biology Letters publication_identifier: issn: - 1744-9561 publication_status: published publisher: The Royal Society publist_id: '7253' quality_controlled: '1' related_material: record: - id: '9847' relation: research_data status: public - id: '202' relation: dissertation_contains status: public scopus_import: '1' status: public title: Effects of mutations in phage restriction sites during escape from restriction–modification type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '818' abstract: - lang: eng text: 'Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ' acknowledgement: 'First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch citation: ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862 apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862 chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862. ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017. ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862. short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:40Z date_published: 2017-09-27T00:00:00Z date_updated: 2023-09-07T12:00:26Z day: '27' ddc: - '571' - '579' degree_awarded: PhD department: - _id: ToBo doi: 10.15479/AT:ISTA:th_862 file: - access_level: closed checksum: da3993c5f90f59a8e8623cc31ad501dd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6210' file_name: Thesis_KarinMitosch.docx file_size: 6331071 relation: source_file - access_level: open_access checksum: 24c3d9e51992f1b721f3df55aa13fcb8 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6211' file_name: Thesis_KarinMitosch.pdf file_size: 9289852 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6831' pubrep_id: '862' related_material: record: - id: '2001' relation: part_of_dissertation status: public - id: '666' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '666' abstract: - lang: eng text: Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors. article_processing_charge: Yes (in subscription journal) author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001 apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001 chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001. ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017. ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403. mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001. short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403. date_created: 2018-12-11T11:47:48Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-07T12:00:25Z day: '26' ddc: - '576' - '610' department: - _id: ToBo - _id: GaTk doi: 10.1016/j.cels.2017.03.001 ec_funded: 1 file: - access_level: open_access checksum: 04ff20011c3d9a601c514aa999a5fe1a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:54Z date_updated: 2020-07-14T12:47:35Z file_id: '5041' file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf file_size: 2438660 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 393 - 403 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Cell Systems publication_identifier: issn: - '24054712' publication_status: published publisher: Cell Press publist_id: '7061' pubrep_id: '901' quality_controlled: '1' related_material: record: - id: '818' relation: dissertation_contains status: public scopus_import: 1 status: public title: Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2017' ... --- _id: '821' abstract: - lang: eng text: "This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games." acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, \ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854 apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854 chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854. ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017. ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854. short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '09' ddc: - '000' degree_awarded: PhD department: - _id: KrCh doi: 10.15479/AT:ISTA:th_854 ec_funded: 1 file: - access_level: open_access checksum: 3a3ec003f6ee73f41f82a544d63dfc77 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:44Z date_updated: 2020-07-14T12:48:10Z file_id: '4900' file_name: IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf file_size: 4103115 relation: main_file - access_level: closed checksum: bd2facc45ff8a2e20c5ed313c2ccaa83 content_type: application/zip creator: dernst date_created: 2019-04-05T07:59:31Z date_updated: 2020-07-14T12:48:10Z file_id: '6201' file_name: 2017_thesis_Pavlogiannis.zip file_size: 14744374 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: '418' project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6828' pubrep_id: '854' related_material: record: - id: '1071' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '1602' relation: part_of_dissertation status: public - id: '1604' relation: part_of_dissertation status: public - id: '1607' relation: part_of_dissertation status: public - id: '1714' 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: Algorithmic advances in program analysis and their applications tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '820' abstract: - lang: eng text: "The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background." acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Fabienne full_name: Jesse, Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse citation: ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857 apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857 chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857. ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017. ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria. mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857. short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-25T00:00:00Z date_updated: 2023-09-07T12:01:21Z day: '25' ddc: - '576' - '577' - '579' degree_awarded: PhD department: - _id: JoBo doi: 10.15479/AT:ISTA:th_857 ec_funded: 1 file: - access_level: open_access checksum: c62257a7bff0c5f39e1abffc6bfcca5c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:00Z date_updated: 2020-07-14T12:48:10Z file_id: '5252' file_name: IST-2017-857-v1+1_thesis_fabienne.pdf file_size: 3417773 relation: main_file - access_level: closed checksum: fc87d7d72fce52824a3ae7dcad0413a8 content_type: application/x-tex creator: dernst date_created: 2019-04-05T08:51:59Z date_updated: 2020-07-14T12:48:10Z file_id: '6212' file_name: 2017_thesis_Jesse_source.tex file_size: 215899 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '87' project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6829' pubrep_id: '857' status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 title: The lac operon in the wild 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '838' abstract: - lang: eng text: 'In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828 apa: Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828 chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828. ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017. ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria. mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828. short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-06-26T00:00:00Z date_updated: 2023-09-07T12:02:28Z day: '26' ddc: - '000' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:th_828 file: - access_level: open_access checksum: ff8639ec4bded6186f44c7bd3ee26804 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:13Z date_updated: 2020-07-14T12:48:12Z file_id: '4799' file_name: IST-2017-828-v1+3_2017_Rybar_thesis.pdf file_size: 847400 relation: main_file - access_level: closed checksum: 3462101745ce8ad199c2d0f75dae4a7e content_type: application/zip creator: dernst date_created: 2019-04-05T08:24:11Z date_updated: 2020-07-14T12:48:12Z file_id: '6202' file_name: 2017_Thesis_Rybar_source.zip file_size: 26054879 relation: source_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6810' pubrep_id: '828' related_material: record: - id: '2082' relation: part_of_dissertation status: public - id: '6196' relation: part_of_dissertation status: public status: public title: (The exact security of) Message authentication codes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6196' abstract: - lang: eng text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem. author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161 apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161 chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161. ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017. ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161. mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161. short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161. date_created: 2019-04-04T13:48:23Z date_published: 2017-02-03T00:00:00Z date_updated: 2023-09-07T12:02:27Z day: '03' ddc: - '000' department: - _id: KrPi doi: 10.13154/TOSC.V2016.I2.145-161 ec_funded: 1 file: - access_level: open_access checksum: f23161d685dd957ae8d7274132999684 content_type: application/pdf creator: dernst date_created: 2019-04-04T13:53:58Z date_updated: 2020-07-14T12:47:24Z file_id: '6197' file_name: 2017_IACR_Gazi.pdf file_size: 597335 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 2016' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 145-161 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: IACR Transactions on Symmetric Cryptology publication_identifier: eissn: - 2519-173X publication_status: published publisher: Ruhr University Bochum quality_controlled: '1' related_material: record: - id: '838' relation: dissertation_contains status: public status: public title: The exact security of PMAC tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2017' ... --- _id: '837' abstract: - lang: eng text: 'The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ' acknowledgement: 'I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Haibing full_name: Xu, Haibing id: 310349D0-F248-11E8-B48F-1D18A9856A87 last_name: Xu citation: ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858 apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858 chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858. ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017. ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858. short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-08-23T00:00:00Z date_updated: 2023-09-07T12:06:38Z day: '23' ddc: - '571' degree_awarded: PhD department: - _id: JoCs doi: 10.15479/AT:ISTA:th_858 file: - access_level: closed checksum: f11925fbbce31e495124b6bc4f10573c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6213' file_name: 2017_Xu_Haibing_Thesis_Source.docx file_size: 3589490 relation: source_file - access_level: open_access checksum: ffb10749a537d615fab1ef0937ccb157 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6214' file_name: 2017_Xu_Thesis_IST.pdf file_size: 11668613 relation: main_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '93' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6811' pubrep_id: '858' related_material: record: - id: '5828' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '938' abstract: - lang: eng text: The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 citation: ama: Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842 apa: Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842 chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842. ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017. ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. mla: Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842. short: M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:18Z date_published: 2017-06-02T00:00:00Z date_updated: 2023-09-07T12:06:09Z day: '02' ddc: - '581' - '583' - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:th_842 file: - access_level: closed checksum: 193425764d9aaaed3ac57062a867b315 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:03:20Z date_updated: 2020-07-14T12:48:15Z file_id: '6215' file_name: 2017_Adamowski-Thesis_Source.docx file_size: 46903863 relation: source_file - access_level: open_access checksum: df5ab01be81f821e1b958596a1ec8d21 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:03:19Z date_updated: 2020-07-14T12:48:15Z file_id: '6216' file_name: 2017_Adamowski-Thesis.pdf file_size: 8698888 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '117' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6483' pubrep_id: '842' related_material: record: - id: '1591' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '992' abstract: - lang: eng text: "An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language)." acknowledgement: FP7/2007-2013/ERC grant agreement no 616160 alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815 apa: Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815 chicago: Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815. ieee: M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017. ista: Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria. mla: Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815. short: M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:35Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-09-07T12:05:41Z day: '01' ddc: - '004' degree_awarded: PhD department: - _id: VlKo doi: 10.15479/AT:ISTA:th_815 ec_funded: 1 file: - access_level: open_access checksum: 81761fb939acb7585c36629f765b4373 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:55Z date_updated: 2020-07-14T12:48:18Z file_id: '4654' file_name: IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf file_size: 786145 relation: main_file - access_level: closed checksum: 2b2d7e1d6c1c79a9795a7aa0f860baf3 content_type: application/zip creator: dernst date_created: 2019-04-05T08:43:24Z date_updated: 2020-07-14T12:48:18Z file_id: '6208' file_name: 2017_Thesis_Rolinek_source.zip file_size: 5936337 relation: source_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '97' project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6407' pubrep_id: '815' status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: Complexity of constraint satisfaction type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '718' abstract: - lang: eng text: Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 - first_name: Matthias full_name: Reitzner, Matthias last_name: Reitzner citation: ama: Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 2017;49(3):745-767. doi:10.1017/apr.2017.20 apa: Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20 chicago: Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20. ieee: H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017. ista: Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767. mla: Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20. short: H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767. date_created: 2018-12-11T11:48:07Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:07:12Z day: '01' department: - _id: HeEd doi: 10.1017/apr.2017.20 ec_funded: 1 external_id: arxiv: - '1607.05915' intvolume: ' 49' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.05915 month: '09' oa: 1 oa_version: Preprint page: 745 - 767 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Advances in Applied Probability publication_identifier: issn: - '00018678' publication_status: published publisher: Cambridge University Press publist_id: '6962' quality_controlled: '1' related_material: record: - id: '6287' relation: dissertation_contains status: public scopus_import: 1 status: public title: Expected sizes of poisson Delaunay mosaics and their discrete Morse functions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2017' ... --- _id: '559' abstract: - lang: eng text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).' alternative_title: - LNCS author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Bram full_name: Cohen, Bram last_name: Cohen - first_name: Danylo full_name: Khilko, Danylo last_name: Khilko - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin citation: ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:10.1007/978-3-319-70697-9_13' apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. https://doi.org/10.1007/978-3-319-70697-9_13' chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13. ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.' ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.' mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13. short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379. conference: end_date: 2017-12-07 location: Hong Kong, China name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security' start_date: 2017-12-03 date_created: 2018-12-11T11:47:10Z date_published: 2017-11-18T00:00:00Z date_updated: 2023-09-07T12:30:22Z day: '18' department: - _id: KrPi doi: 10.1007/978-3-319-70697-9_13 ec_funded: 1 intvolume: ' 10625' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/893.pdf month: '11' oa: 1 oa_version: Submitted Version page: 357 - 379 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331970696-2 publication_status: published publisher: Springer publist_id: '7257' quality_controlled: '1' related_material: record: - id: '83' relation: dissertation_contains status: public scopus_import: 1 status: public title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10625 year: '2017' ... --- _id: '550' abstract: - lang: eng text: For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities. article_number: '63' author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97 apa: Alt, J. (2017). Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-ECP97 chicago: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-ECP97. ieee: J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63. mla: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:10.1214/17-ECP97. short: J. Alt, Electronic Communications in Probability 22 (2017). date_created: 2018-12-11T11:47:07Z date_published: 2017-11-21T00:00:00Z date_updated: 2023-09-07T12:38:08Z day: '21' ddc: - '539' department: - _id: LaEr doi: 10.1214/17-ECP97 ec_funded: 1 file: - access_level: open_access checksum: 0ec05303a0de190de145654237984c79 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:04Z date_updated: 2020-07-14T12:47:00Z file_id: '4663' file_name: IST-2018-926-v1+1_euclid.ecp.1511233247.pdf file_size: 470876 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_identifier: issn: - 1083589X publication_status: published publisher: Institute of Mathematical Statistics publist_id: '7265' pubrep_id: '926' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: 1 status: public title: Singularities of the density of states of random Gram matrices 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: 22 year: '2017' ... --- _id: '647' abstract: - lang: eng text: Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems. alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - 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: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 citation: ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7' apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7' chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7. ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.' ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.' mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol. 10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7. short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'FORMATS: Formal Modelling and Analysis of Timed Systems' start_date: 2017-09-05 date_created: 2018-12-11T11:47:41Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-319-65765-3_7 file: - access_level: open_access checksum: faf546914ba29bcf9974ee36b6b16750 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:38Z date_updated: 2020-07-14T12:47:31Z file_id: '4956' file_name: IST-2017-831-v1+1_main.pdf file_size: 3806864 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 116 - 132 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-331965764-6 publication_status: published publisher: Springer publist_id: '7129' pubrep_id: '831' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Conic abstractions for hybrid systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '10419 ' year: '2017' ... --- _id: '631' abstract: - lang: eng text: Template polyhedra generalize intervals and octagons to polyhedra whose facets are orthogonal to a given set of arbitrary directions. They have been employed in the abstract interpretation of programs and, with particular success, in the reachability analysis of hybrid automata. While previously, the choice of directions has been left to the user or a heuristic, we present a method for the automatic discovery of directions that generalize and eliminate spurious counterexamples. We show that for the class of convex hybrid automata, i.e., hybrid automata with (possibly nonlinear) convex constraints on derivatives, such directions always exist and can be found using convex optimization. We embed our method inside a CEGAR loop, thus enabling the time-unbounded reachability analysis of an important and richer class of hybrid automata than was previously possible. We evaluate our method on several benchmarks, demonstrating also its superior efficiency for the special case of linear hybrid automata. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project DP140104219 (Robust AI Planning for Hybrid Systems). alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34' apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34' chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger. “Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_34. ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 589–606.' ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 589–606.' mla: Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra. Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34. short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017, pp. 589–606. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2017-04-22 date_created: 2018-12-11T11:47:36Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '31' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-54577-5_34 file: - access_level: open_access checksum: f395d0d20102b89aeaad8b4ef4f18f4f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:41Z date_updated: 2020-07-14T12:47:27Z file_id: '4897' file_name: IST-2017-741-v1+1_main.pdf file_size: 569863 relation: main_file - access_level: open_access checksum: f416ee1ae4497b23ecdf28b1f18bb8df content_type: application/pdf creator: system date_created: 2018-12-12T10:11:42Z date_updated: 2020-07-14T12:47:27Z file_id: '4898' file_name: IST-2018-741-v2+2_main.pdf file_size: 563276 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 10205' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 589 - 606 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-366254576-8 publication_status: published publisher: Springer publist_id: '7162' pubrep_id: '966' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Counterexample guided refinement of template polyhedra type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10205 year: '2017' ... --- _id: '1144' abstract: - lang: eng text: We show that matrix elements of functions of N × N Wigner matrices fluctuate on a scale of order N−1/2 and we identify the limiting fluctuation. Our result holds for any function f of the matrix that has bounded variation thus considerably relaxing the regularity requirement imposed in [7, 11]. acknowledgement: Partially supported by the IST Austria Excellence Scholarship. article_number: '86' author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 2017;21. doi:10.1214/16-ECP38 apa: Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-ECP38 chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-ECP38. ieee: L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,” Electronic Communications in Probability, vol. 21. Institute of Mathematical Statistics, 2017. ista: Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 21, 86. mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute of Mathematical Statistics, 2017, doi:10.1214/16-ECP38. short: L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017). date_created: 2018-12-11T11:50:23Z date_published: 2017-01-02T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '02' ddc: - '510' department: - _id: LaEr doi: 10.1214/16-ECP38 ec_funded: 1 file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:18:10Z date_updated: 2018-12-12T10:18:10Z file_id: '5329' file_name: IST-2017-747-v1+1_euclid.ecp.1483347665.pdf file_size: 440770 relation: main_file file_date_updated: 2018-12-12T10:18:10Z has_accepted_license: '1' intvolume: ' 21' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6214' pubrep_id: '747' quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public scopus_import: 1 status: public title: Fluctuations of functions of Wigner matrices 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: 21 year: '2017' ... --- _id: '486' abstract: - lang: eng text: Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut. article_number: '241' article_processing_charge: No article_type: original author: - first_name: Oskar full_name: Elek, Oskar last_name: Elek - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Jaroslav full_name: Krivanek, Jaroslav last_name: Krivanek citation: ama: Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890 apa: Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., … Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890 chicago: Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890. ieee: O. Elek et al., “Scattering-aware texture reproduction for 3D printing,” ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017. ista: Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 36(6), 241. mla: Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890. short: O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie, J. Krivanek, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:44Z date_published: 2017-11-20T00:00:00Z date_updated: 2023-09-07T13:11:15Z day: '20' ddc: - '003' - '000' - '005' department: - _id: BeBi doi: 10.1145/3130800.3130890 ec_funded: 1 file: - access_level: open_access checksum: 48386fa6956c3645fc89594dc898b147 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:46Z date_updated: 2020-07-14T12:46:35Z file_id: '4836' file_name: IST-2018-1052-v1+1_ElekSumin2017SGA.pdf file_size: 107349827 relation: main_file - access_level: open_access checksum: 21c89c28fb8d70f6602f752bf997aa0f content_type: application/pdf creator: bbickel date_created: 2019-12-16T14:48:57Z date_updated: 2020-07-14T12:46:35Z file_id: '7189' file_name: ElekSumin2017SGA_reduced_file_size.pdf file_size: 4683145 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 36' issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7334' pubrep_id: '1052' quality_controlled: '1' related_material: record: - id: '8386' relation: dissertation_contains status: public scopus_import: 1 status: public title: Scattering-aware texture reproduction for 3D printing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '637' abstract: - lang: eng text: For many cryptographic primitives, it is relatively easy to achieve selective security (where the adversary commits a-priori to some of the choices to be made later in the attack) but appears difficult to achieve the more natural notion of adaptive security (where the adversary can make all choices on the go as the attack progresses). A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption (Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b). Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework that connects all of these works and allows us to present them in a unified and simplified fashion. Moreover, we use the framework to derive a new result for adaptively secure secret sharing over access structures defined via monotone circuits. We envision that further applications will follow in the future. Underlying our framework is the following simple idea. It is well known that selective security, where the adversary commits to n-bits of information about his future choices, automatically implies adaptive security at the cost of amplifying the adversary’s advantage by a factor of up to 2n. However, in some cases the proof of selective security proceeds via a sequence of hybrids, where each pair of adjacent hybrids locally only requires some smaller partial information consisting of m ≪ n bits. The partial information needed might be completely different between different pairs of hybrids, and if we look across all the hybrids we might rely on the entire n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security, at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n. In all of our examples using the above framework, the different hybrids are captured by some sort of a graph pebbling game and the amount of information that the adversary needs to commit to in each pair of hybrids is bounded by the maximum number of pebbles in play at any point in time. Therefore, coming up with better strategies for proving adaptive security translates to various pebbling strategies for different types of graphs. alternative_title: - LNCS author: - first_name: Zahra full_name: Jafargholi, Zahra last_name: Jafargholi - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Ilan full_name: Komargodski, Ilan last_name: Komargodski - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer; 2017:133-163. doi:10.1007/978-3-319-63688-7_5' apa: 'Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak, K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz & H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5' chicago: Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski, Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5. ieee: 'Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak, and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.' ista: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401, 133–163.' mla: Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5. short: Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak, D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163. conference: end_date: 2017-07-24 location: Santa Barbara, CA, United States name: 'CRYPTO: Cryptology' start_date: 2017-07-20 date_created: 2018-12-11T11:47:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-07T13:32:11Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-63688-7_5 ec_funded: 1 editor: - first_name: Jonathan full_name: Katz, Jonathan last_name: Katz - first_name: Hovav full_name: Shacham, Hovav last_name: Shacham intvolume: ' 10401' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/515 month: '01' oa: 1 oa_version: Submitted Version page: 133 - 163 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331963687-0 publication_status: published publisher: Springer publist_id: '7151' quality_controlled: '1' related_material: record: - id: '10035' relation: dissertation_contains status: public scopus_import: 1 status: public title: Be adaptive avoid overcommitting type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10401 year: '2017' ... --- _id: '9842' abstract: - lang: eng text: Mathematica notebooks used to generate figures. article_processing_charge: No author: - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1' apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1' chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.' ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.' ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.' mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.' short: A. Etheridge, N.H. Barton, (2017). date_created: 2021-08-09T13:18:55Z date_published: 2017-12-29T00:00:00Z date_updated: 2023-09-11T13:41:21Z day: '29' department: - _id: NiBa doi: 10.17632/nw68fxzjpm.1 main_file_link: - open_access: '1' url: https://doi.org/10.17632/nw68fxzjpm.1 month: '12' oa: 1 oa_version: Published Version publisher: Mendeley Data related_material: record: - id: '564' relation: used_in_publication status: public status: public title: 'Data for: Establishment in a new habitat by polygenic adaptation' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '14206' abstract: - lang: eng text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings. article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: Advances in Neural Information Processing Systems. ; 2017.' apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In Advances in Neural Information Processing Systems. Long Beach, CA, United States. chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In Advances in Neural Information Processing Systems, 2017. ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017. ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.' mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017. short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017. conference: end_date: 2017-12-09 location: Long Beach, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2017-12-04 date_created: 2023-08-22T14:17:38Z date_published: 2017-05-31T00:00:00Z date_updated: 2023-09-13T08:32:23Z day: '31' department: - _id: FrLo extern: '1' external_id: arxiv: - '1705.11041' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.11041 month: '05' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781510860964' publication_status: published quality_controlled: '1' status: public title: Greedy algorithms for cone constrained optimization with convergence guarantees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '14205' abstract: - lang: eng text: Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions. article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Rajiv full_name: Khanna, Rajiv last_name: Khanna - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Vol 54. ML Research Press; 2017:860-868.' apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.' chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 54:860–68. ML Research Press, 2017. ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868. ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.' mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017, pp. 860–68. short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868. conference: end_date: 2017-04-22 location: Fort Lauderdale, FL, United States name: 'AISTATS: Conference on Artificial Intelligence and Statistics' start_date: 2017-04-20 date_created: 2023-08-22T14:17:19Z date_published: 2017-02-21T00:00:00Z date_updated: 2023-09-13T09:49:10Z day: '21' department: - _id: FrLo extern: '1' external_id: arxiv: - '1702.06457' intvolume: ' 54' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1702.06457 month: '02' oa: 1 oa_version: Preprint page: 860-868 publication: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: A unified optimization view on generalized matching pursuit and Frank-Wolfe type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 54 year: '2017' ... --- _id: '202' abstract: - lang: eng text: 'Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.' acknowledgement: "During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 citation: ama: Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916 apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916 chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916. ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017. ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916. short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:45:10Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-15T12:04:56Z day: '01' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:th_916 file: - access_level: open_access checksum: 33cfb59674e91f82e3738396d3fb3776 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:48Z date_updated: 2020-07-14T12:45:24Z file_id: '4710' file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf file_size: 18569590 relation: main_file - access_level: closed checksum: dcc239968decb233e7f98cf1083d8c26 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:33:14Z date_updated: 2020-07-14T12:45:24Z file_id: '6204' file_name: 2017_Pleska_Maros_Thesis.docx file_size: 2801649 relation: source_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '126' project: - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7711' pubrep_id: '916' related_material: record: - id: '1243' relation: part_of_dissertation status: public - id: '561' relation: part_of_dissertation status: public - id: '457' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Biology of restriction-modification systems at the single-cell and population level 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6287' abstract: - lang: eng text: The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873 apa: Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873 chicago: Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873. ieee: A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017. ista: Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria. mla: Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873. short: A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017. date_created: 2019-04-09T15:04:32Z date_published: 2017-10-27T00:00:00Z date_updated: 2023-09-15T12:10:34Z day: '27' ddc: - '514' - '516' - '519' degree_awarded: PhD department: - _id: HeEd doi: 10.15479/AT:ISTA:th_873 file: - access_level: open_access checksum: ece7e598a2f060b263c2febf7f3fe7f9 content_type: application/pdf creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6289' file_name: 2017_Thesis_Nikitenko.pdf file_size: 2324870 relation: main_file - access_level: closed checksum: 99b7ad76e317efd447af60f91e29b49b content_type: application/zip creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6290' file_name: 2017_Thesis_Nikitenko_source.zip file_size: 2863219 relation: source_file file_date_updated: 2020-07-14T12:47:26Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria pubrep_id: '873' related_material: record: - id: '718' relation: part_of_dissertation status: public - id: '5678' relation: part_of_dissertation status: public - id: '87' 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: 'Discrete Morse theory for random complexes ' 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ...