--- _id: '13079' abstract: - lang: eng text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs. article_processing_charge: No author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Hsiao full_name: Tsai, Hsiao last_name: Tsai - first_name: Juliana full_name: Capitanio, Juliana last_name: Capitanio - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: 'Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. 2019. doi:10.5061/DRYAD.N0R525H' apa: 'Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. Dryad. https://doi.org/10.5061/DRYAD.N0R525H' chicago: 'Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.' ieee: 'A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress.” Dryad, 2019.' ista: 'Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress, Dryad, 10.5061/DRYAD.N0R525H.' mla: 'Buchwalter, Abigail, et al. Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress. Dryad, 2019, doi:10.5061/DRYAD.N0R525H.' short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, (2019). date_created: 2023-05-23T17:09:30Z date_published: 2019-10-28T00:00:00Z date_updated: 2023-05-31T06:36:23Z day: '28' ddc: - '570' doi: 10.5061/DRYAD.N0R525H extern: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.n0r525h month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '11060' relation: used_in_publication status: public status: public title: 'Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6989' abstract: - lang: eng text: 'When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. ' acknowledgement: This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere. article_processing_charge: No author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Hugo A full_name: Akitaya, Hugo A last_name: Akitaya - first_name: Kenneth C full_name: Cheung, Kenneth C last_name: Cheung - first_name: Erik D full_name: Demaine, Erik D last_name: Demaine - first_name: Martin L full_name: Demaine, Martin L last_name: Demaine - first_name: Sandor P full_name: Fekete, Sandor P last_name: Fekete - first_name: Linda full_name: Kleist, Linda last_name: Kleist - first_name: Irina full_name: Kostitsyna, Irina last_name: Kostitsyna - first_name: Maarten full_name: Löffler, Maarten last_name: Löffler - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Klara full_name: Mundilova, Klara last_name: Mundilova - first_name: Christiane full_name: Schmidt, Christiane last_name: Schmidt citation: ama: 'Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.' apa: 'Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.' chicago: Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019. ieee: O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170. ista: 'Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.' mla: Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70. short: O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170. conference: end_date: 2019-08-10 location: Edmonton, Canada name: 'CCCG: Canadian Conference in Computational Geometry' start_date: 2019-08-08 date_created: 2019-11-04T16:46:11Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-04T10:57:42Z day: '01' department: - _id: HeEd external_id: arxiv: - '1910.09917' language: - iso: eng main_file_link: - open_access: '1' url: https://cccg.ca/proceedings/2019/proceedings.pdf month: '08' oa: 1 oa_version: Published Version page: 164-170 publication: Proceedings of the 31st Canadian Conference on Computational Geometry publication_status: published publisher: Canadian Conference on Computational Geometry quality_controlled: '1' related_material: record: - id: '8317' relation: extended_version status: public scopus_import: '1' status: public title: Folding polyominoes with holes into a cube type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 year: '2019' ... --- _id: '13366' abstract: - lang: eng text: The ability to reversibly assemble nanoparticles using light is both fundamentally interesting and important for applications ranging from reversible data storage to controlled drug delivery. Here, the diverse approaches that have so far been developed to control the self-assembly of nanoparticles using light are reviewed and compared. These approaches include functionalizing nanoparticles with monolayers of photoresponsive molecules, placing them in photoresponsive media capable of reversibly protonating the particles under light, and decorating plasmonic nanoparticles with thermoresponsive polymers, to name just a few. The applicability of these methods to larger, micrometer-sized particles is also discussed. Finally, several perspectives on further developments in the field are offered. article_number: '1905866' article_processing_charge: No article_type: original author: - first_name: Tong full_name: Bian, Tong last_name: Bian - first_name: Zonglin full_name: Chu, Zonglin last_name: Chu - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Bian T, Chu Z, Klajn R. The many ways to assemble nanoparticles using light. Advanced Materials. 2019;32(20). doi:10.1002/adma.201905866 apa: Bian, T., Chu, Z., & Klajn, R. (2019). The many ways to assemble nanoparticles using light. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201905866 chicago: Bian, Tong, Zonglin Chu, and Rafal Klajn. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials. Wiley, 2019. https://doi.org/10.1002/adma.201905866. ieee: T. Bian, Z. Chu, and R. Klajn, “The many ways to assemble nanoparticles using light,” Advanced Materials, vol. 32, no. 20. Wiley, 2019. ista: Bian T, Chu Z, Klajn R. 2019. The many ways to assemble nanoparticles using light. Advanced Materials. 32(20), 1905866. mla: Bian, Tong, et al. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials, vol. 32, no. 20, 1905866, Wiley, 2019, doi:10.1002/adma.201905866. short: T. Bian, Z. Chu, R. Klajn, Advanced Materials 32 (2019). date_created: 2023-08-01T09:37:26Z date_published: 2019-11-19T00:00:00Z date_updated: 2023-08-07T10:23:41Z day: '19' doi: 10.1002/adma.201905866 extern: '1' external_id: pmid: - '31709655' intvolume: ' 32' issue: '20' keyword: - Mechanical Engineering - Mechanics of Materials - General Materials Science language: - iso: eng month: '11' oa_version: None pmid: 1 publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: The many ways to assemble nanoparticles using light type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2019' ... --- _id: '13373' abstract: - lang: eng text: The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments. article_processing_charge: No article_type: original author: - first_name: Zonglin full_name: Chu, Zonglin last_name: Chu - first_name: Yanxiao full_name: Han, Yanxiao last_name: Han - first_name: Tong full_name: Bian, Tong last_name: Bian - first_name: Soumen full_name: De, Soumen last_name: De - first_name: Petr full_name: Král, Petr last_name: Král - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 2019;141(5):1949-1960. doi:10.1021/jacs.8b09638 apa: Chu, Z., Han, Y., Bian, T., De, S., Král, P., & Klajn, R. (2019). Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09638 chicago: Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09638. ieee: Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control of azobenzene switching on nanoparticles,” Journal of the American Chemical Society, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019. ista: Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 141(5), 1949–1960. mla: Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society, vol. 141, no. 5, American Chemical Society, 2019, pp. 1949–60, doi:10.1021/jacs.8b09638. short: Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American Chemical Society 141 (2019) 1949–1960. date_created: 2023-08-01T09:39:19Z date_published: 2019-02-06T00:00:00Z date_updated: 2023-08-07T10:51:12Z day: '06' doi: 10.1021/jacs.8b09638 extern: '1' external_id: pmid: - '30595017' intvolume: ' 141' issue: '5' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '02' oa_version: Published Version page: 1949-1960 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: Supramolecular control of azobenzene switching on nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2019' ... --- _id: '13372' abstract: - lang: eng text: 'The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.' article_processing_charge: No article_type: original author: - first_name: Marek full_name: Grzelczak, Marek last_name: Grzelczak - first_name: Luis M. full_name: Liz-Marzán, Luis M. last_name: Liz-Marzán - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 2019;48(5):1342-1361. doi:10.1039/c8cs00787j apa: Grzelczak, M., Liz-Marzán, L. M., & Klajn, R. (2019). Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c8cs00787j chicago: Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8cs00787j. ieee: M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly of nanoparticles,” Chemical Society Reviews, vol. 48, no. 5. Royal Society of Chemistry, pp. 1342–1361, 2019. ista: Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361. mla: Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews, vol. 48, no. 5, Royal Society of Chemistry, 2019, pp. 1342–61, doi:10.1039/c8cs00787j. short: M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 1342–1361. date_created: 2023-08-01T09:38:52Z date_published: 2019-01-28T00:00:00Z date_updated: 2023-08-07T10:48:31Z day: '28' doi: 10.1039/c8cs00787j extern: '1' external_id: pmid: - '30688963' intvolume: ' 48' issue: '5' keyword: - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1039/C8CS00787J month: '01' oa: 1 oa_version: Published Version page: 1342-1361 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: Stimuli-responsive self-assembly of nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2019' ... --- _id: '13369' abstract: - lang: eng text: Arylazopyrazoles represent a new family of molecular photoswitches characterized by a near-quantitative conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography have independently demonstrated that each cage can encapsulate two molecules of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage. article_processing_charge: No article_type: original author: - first_name: Anton I full_name: Hanopolskyi, Anton I last_name: Hanopolskyi - first_name: Soumen full_name: De, Soumen last_name: De - first_name: Michał J full_name: Białek, Michał J last_name: Białek - first_name: Yael full_name: Diskin-Posner, Yael last_name: Diskin-Posner - first_name: Liat full_name: Avram, Liat last_name: Avram - first_name: Moran full_name: Feller, Moran last_name: Feller - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Hanopolskyi AI, De S, Białek MJ, et al. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 2019;15:2398-2407. doi:10.3762/bjoc.15.232 apa: Hanopolskyi, A. I., De, S., Białek, M. J., Diskin-Posner, Y., Avram, L., Feller, M., & Klajn, R. (2019). Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.15.232 chicago: Hanopolskyi, Anton I, Soumen De, Michał J Białek, Yael Diskin-Posner, Liat Avram, Moran Feller, and Rafal Klajn. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry. Beilstein Institut, 2019. https://doi.org/10.3762/bjoc.15.232. ieee: A. I. Hanopolskyi et al., “Reversible switching of arylazopyrazole within a metal–organic cage,” Beilstein Journal of Organic Chemistry, vol. 15. Beilstein Institut, pp. 2398–2407, 2019. ista: Hanopolskyi AI, De S, Białek MJ, Diskin-Posner Y, Avram L, Feller M, Klajn R. 2019. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 15, 2398–2407. mla: Hanopolskyi, Anton I., et al. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry, vol. 15, Beilstein Institut, 2019, pp. 2398–407, doi:10.3762/bjoc.15.232. short: A.I. Hanopolskyi, S. De, M.J. Białek, Y. Diskin-Posner, L. Avram, M. Feller, R. Klajn, Beilstein Journal of Organic Chemistry 15 (2019) 2398–2407. date_created: 2023-08-01T09:38:06Z date_published: 2019-10-10T00:00:00Z date_updated: 2023-08-07T10:34:56Z day: '10' doi: 10.3762/bjoc.15.232 extern: '1' external_id: pmid: - '31666874' intvolume: ' 15' keyword: - Organic Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3762/bjoc.15.232 month: '10' oa: 1 oa_version: Published Version page: 2398-2407 pmid: 1 publication: Beilstein Journal of Organic Chemistry publication_identifier: eissn: - 1860-5397 publication_status: published publisher: Beilstein Institut quality_controlled: '1' scopus_import: '1' status: public title: Reversible switching of arylazopyrazole within a metal–organic cage type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2019' ... --- _id: '13370' abstract: - lang: eng text: Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows. article_processing_charge: No article_type: original author: - first_name: Zonglin full_name: Chu, Zonglin last_name: Chu - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Chu Z, Klajn R. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 2019;19(10):7106-7111. doi:10.1021/acs.nanolett.9b02642 apa: Chu, Z., & Klajn, R. (2019). Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b02642 chicago: Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b02642. ieee: Z. Chu and R. Klajn, “Polysilsesquioxane nanowire networks as an ‘Artificial Solvent’ for reversible operation of photochromic molecules,” Nano Letters, vol. 19, no. 10. American Chemical Society, pp. 7106–7111, 2019. ista: Chu Z, Klajn R. 2019. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 19(10), 7106–7111. mla: Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters, vol. 19, no. 10, American Chemical Society, 2019, pp. 7106–11, doi:10.1021/acs.nanolett.9b02642. short: Z. Chu, R. Klajn, Nano Letters 19 (2019) 7106–7111. date_created: 2023-08-01T09:38:23Z date_published: 2019-09-20T00:00:00Z date_updated: 2023-08-07T10:39:34Z day: '20' doi: 10.1021/acs.nanolett.9b02642 extern: '1' external_id: pmid: - '31539469' intvolume: ' 19' issue: '10' keyword: - Mechanical Engineering - Condensed Matter Physics - General Materials Science - General Chemistry - Bioengineering language: - iso: eng month: '09' oa_version: None page: 7106-7111 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '13371' abstract: - lang: eng text: Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials. article_processing_charge: No article_type: original author: - first_name: Michał J. full_name: Białek, Michał J. last_name: Białek - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn citation: ama: Białek MJ, Klajn R. Diamond grows up. Chem. 2019;5(9):2283-2285. doi:10.1016/j.chempr.2019.08.012 apa: Białek, M. J., & Klajn, R. (2019). Diamond grows up. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2019.08.012 chicago: Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem. Elsevier, 2019. https://doi.org/10.1016/j.chempr.2019.08.012. ieee: M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019. ista: Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285. mla: Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:10.1016/j.chempr.2019.08.012. short: M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285. date_created: 2023-08-01T09:38:38Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-07T10:46:50Z day: '12' doi: 10.1016/j.chempr.2019.08.012 extern: '1' intvolume: ' 5' issue: '9' keyword: - Materials Chemistry - Biochemistry (medical) - General Chemical Engineering - Environmental Chemistry - Biochemistry - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.chempr.2019.08.012 month: '09' oa: 1 oa_version: Published Version page: 2283-2285 publication: Chem publication_identifier: eissn: - 2451-9294 issn: - 2451-9308 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Diamond grows up type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2019' ... --- _id: '6884' abstract: - lang: eng text: 'In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players'' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ' alternative_title: - LIPIcs article_number: '11' 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: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic citation: ama: 'Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11' apa: 'Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11' chicago: Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11. ieee: 'G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.' ista: 'Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.' mla: Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11. short: G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Aachen, Germany name: 'MFCS: nternational Symposium on Mathematical Foundations of Computer Science' start_date: 2019-08-26 date_created: 2019-09-18T08:04:26Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-07T14:08:34Z day: '01' ddc: - '004' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPICS.MFCS.2019.11 ec_funded: 1 external_id: arxiv: - '1905.03835' file: - access_level: open_access checksum: 6346e116a4f4ed1414174d96d2c4fbd7 content_type: application/pdf creator: kschuh date_created: 2019-09-27T11:45:15Z date_updated: 2020-07-14T12:47:42Z file_id: '6913' file_name: 2019_LIPIcs_Avni.pdf file_size: 554457 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 138' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '08' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9239' relation: later_version status: public scopus_import: 1 status: public title: Bidding mechanisms in graph games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 138 year: '2019' ... --- _id: '13471' abstract: - lang: eng text: We perform an extensive numerical study of the evolution of massive binary systems to predict the peculiar velocities that stars obtain when their companion collapses and disrupts the system. Our aim is to (i) identify which predictions are robust against model uncertainties and assess their implications, (ii) investigate which physical processes leave a clear imprint and may therefore be constrained observationally, and (iii) provide a suite of publicly available model predictions to allow for the use of kinematic constraints from the Gaia mission. We find that 22+26−8% of all massive binary systems merge prior to the first core-collapse in the system. Of the remainder, 86+11−9% become unbound because of the core-collapse. Remarkably, this rarely produces runaway stars (observationally defined as stars with velocities above 30 km s−1). These are outnumbered by more than an order of magnitude by slower unbound companions, or “walkaway stars”. This is a robust outcome of our simulations and is due to the reversal of the mass ratio prior to the explosion and widening of the orbit, as we show analytically and numerically. For stars more massive than 15 M⊙, we estimate that 10+5−8% are walkaways and only 0.5+1.0−0.4% are runaways, nearly all of which have accreted mass from their companion. Our findings are consistent with earlier studies; however, the low runaway fraction we find is in tension with observed fractions of about 10%. Thus, astrometric data on presently single massive stars can potentially constrain the physics of massive binary evolution. Finally, we show that the high end of the mass distributions of runaway stars is very sensitive to the assumed black hole natal kicks, and we propose this as a potentially stringent test for the explosion mechanism. We also discuss companions remaining bound that can evolve into X-ray and gravitational wave sources. article_number: A66 article_processing_charge: No article_type: original author: - first_name: M. full_name: Renzo, M. last_name: Renzo - 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: 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. full_name: Justham, S. last_name: Justham - first_name: R. J. full_name: Farmer, R. J. last_name: Farmer - first_name: R. G. full_name: Izzard, R. G. last_name: Izzard - first_name: S. full_name: Toonen, S. last_name: Toonen - first_name: H. full_name: Sana, H. last_name: Sana citation: ama: Renzo M, Zapartas E, de Mink SE, et al. Massive runaway and walkaway stars. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201833297 apa: Renzo, M., Zapartas, E., de Mink, S. E., Götberg, Y. L. L., Justham, S., Farmer, R. J., … Sana, H. (2019). Massive runaway and walkaway stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833297 chicago: Renzo, M., E. Zapartas, S. E. de Mink, Ylva Louise Linsdotter Götberg, S. Justham, R. J. Farmer, R. G. Izzard, S. Toonen, and H. Sana. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833297. ieee: M. Renzo et al., “Massive runaway and walkaway stars,” Astronomy & Astrophysics, vol. 624. EDP Sciences, 2019. ista: Renzo M, Zapartas E, de Mink SE, Götberg YLL, Justham S, Farmer RJ, Izzard RG, Toonen S, Sana H. 2019. Massive runaway and walkaway stars. Astronomy & Astrophysics. 624, A66. mla: Renzo, M., et al. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics, vol. 624, A66, EDP Sciences, 2019, doi:10.1051/0004-6361/201833297. short: M. Renzo, E. Zapartas, S.E. de Mink, Y.L.L. Götberg, S. Justham, R.J. Farmer, R.G. Izzard, S. Toonen, H. Sana, Astronomy & Astrophysics 624 (2019). date_created: 2023-08-03T10:14:18Z date_published: 2019-04-11T00:00:00Z date_updated: 2023-08-09T12:26:08Z day: '11' doi: 10.1051/0004-6361/201833297 extern: '1' external_id: arxiv: - '1804.09164' intvolume: ' 624' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201833297 month: '04' 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: Massive runaway and walkaway stars type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 624 year: '2019' ... --- _id: '13470' abstract: - lang: eng text: "Context. Massive Wolf–Rayet (WR) stars dominate the radiative and mechanical energy budget of galaxies and probe a critical phase in the evolution of massive stars prior to core collapse. It is not known whether core He-burning WR stars (classical WR; cWR) form predominantly through wind stripping (w-WR) or binary stripping (b-WR). Whereas spectroscopy of WR binaries has so-far largely been avoided because of its complexity, our study focuses on the 44 WR binaries and binary candidates of the Large Magellanic Cloud (LMC; metallicity Z ≈ 0.5 Z⊙), which were identified on the basis of radial velocity variations, composite spectra, or high X-ray luminosities.\r\n\r\nAims. Relying on a diverse spectroscopic database, we aim to derive the physical and orbital parameters of our targets, confronting evolution models of evolved massive stars at subsolar metallicity and constraining the impact of binary interaction in forming these stars.\r\n\r\nMethods. Spectroscopy was performed using the Potsdam Wolf–Rayet (PoWR) code and cross-correlation techniques. Disentanglement was performed using the code Spectangular or the shift-and-add algorithm. Evolutionary status was interpreted using the Binary Population and Spectral Synthesis (BPASS) code, exploring binary interaction and chemically homogeneous evolution.\r\n\r\nResults. Among our sample, 28/44 objects show composite spectra and are analyzed as such. An additional five targets show periodically moving WR primaries but no detected companions (SB1); two (BAT99 99 and 112) are potential WR + compact-object candidates owing to their high X-ray luminosities. We cannot confirm the binary nature of the remaining 11 candidates. About two-thirds of the WN components in binaries are identified as cWR, and one-third as hydrogen-burning WR stars. We establish metallicity-dependent mass-loss recipes, which broadly agree with those recently derived for single WN stars, and in which so-called WN3/O3 stars are clear outliers. We estimate that 45  ±  30% of the cWR stars in our sample have interacted with a companion via mass transfer. However, only ≈12  ±  7% of the cWR stars in our sample naively appear to have formed purely owing to stripping via a companion (12% b-WR). Assuming that apparently single WR stars truly formed as single stars, this comprises ≈4% of the whole LMC WN population, which is about ten times less than expected. No obvious differences in the properties of single and binary WN stars, whose luminosities extend down to log L ≈ 5.2 [L⊙], are apparent. With the exception of a few systems (BAT99 19, 49, and 103), the equatorial rotational velocities of the OB-type companions are moderate (veq ≲ 250 km s−1) and challenge standard formalisms of angular-momentum accretion. For most objects, chemically homogeneous evolution can be rejected for the secondary, but not for the WR progenitor.\r\n\r\nConclusions. No obvious dichotomy in the locations of apparently single and binary WN stars on the Hertzsprung-Russell diagram is apparent. According to commonly used stellar evolution models (BPASS, Geneva), most apparently single WN stars could not have formed as single stars, implying that they were stripped by an undetected companion. Otherwise, it must follow that pre-WR mass-loss/mixing (e.g., during the red supergiant phase) are strongly underestimated in standard stellar evolution models." article_number: A151 article_processing_charge: No article_type: original author: - first_name: T. full_name: Shenar, T. last_name: Shenar - first_name: D. P. full_name: Sablowski, D. P. last_name: Sablowski - first_name: R. full_name: Hainich, R. last_name: Hainich - first_name: H. full_name: Todt, H. last_name: Todt - first_name: A. F. J. full_name: Moffat, A. F. J. last_name: Moffat - first_name: L. M. full_name: Oskinova, L. M. last_name: Oskinova - first_name: V. full_name: Ramachandran, V. last_name: Ramachandran - first_name: H. full_name: Sana, H. last_name: Sana - first_name: A. A. C. full_name: Sander, A. A. C. last_name: Sander - first_name: O. full_name: Schnurr, O. last_name: Schnurr - first_name: N. full_name: St-Louis, N. last_name: St-Louis - first_name: D. full_name: Vanbeveren, D. last_name: Vanbeveren - 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: W.-R. full_name: Hamann, W.-R. last_name: Hamann citation: ama: Shenar T, Sablowski DP, Hainich R, et al. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 2019;627. doi:10.1051/0004-6361/201935684 apa: Shenar, T., Sablowski, D. P., Hainich, R., Todt, H., Moffat, A. F. J., Oskinova, L. M., … Hamann, W.-R. (2019). The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935684 chicago: Shenar, T., D. P. Sablowski, R. Hainich, H. Todt, A. F. J. Moffat, L. M. Oskinova, V. Ramachandran, et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935684. ieee: T. Shenar et al., “The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud,” Astronomy & Astrophysics, vol. 627. EDP Sciences, 2019. ista: Shenar T, Sablowski DP, Hainich R, Todt H, Moffat AFJ, Oskinova LM, Ramachandran V, Sana H, Sander AAC, Schnurr O, St-Louis N, Vanbeveren D, Götberg YLL, Hamann W-R. 2019. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 627, A151. mla: Shenar, T., et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics, vol. 627, A151, EDP Sciences, 2019, doi:10.1051/0004-6361/201935684. short: T. Shenar, D.P. Sablowski, R. Hainich, H. Todt, A.F.J. Moffat, L.M. Oskinova, V. Ramachandran, H. Sana, A.A.C. Sander, O. Schnurr, N. St-Louis, D. Vanbeveren, Y.L.L. Götberg, W.-R. Hamann, Astronomy & Astrophysics 627 (2019). date_created: 2023-08-03T10:14:09Z date_published: 2019-07-16T00:00:00Z date_updated: 2023-08-09T12:29:58Z day: '16' doi: 10.1051/0004-6361/201935684 extern: '1' intvolume: ' 627' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201935684 month: '07' 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' related_material: link: - relation: erratum url: https://doi.org/10.1051/0004-6361/201935684e scopus_import: '1' status: public title: The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 627 year: '2019' ... --- _id: '13472' abstract: - lang: eng text: Massive stars in binaries can give rise to extreme phenomena such as X-ray binaries and gravitational wave sources after one or both stars end their lives as core-collapse supernovae. Stars in close orbit around a stellar or compact companion are expected to explode as “stripped-envelope supernovae”, showing no (Type Ib/c) or little (Type IIb) signs of hydrogen in the spectra, because hydrogen-rich progenitors are too large to fit. The physical processes responsible for the stripping process and the fate of the companion are still very poorly understood. Aiming to find new clues, we investigate Cas A, which is a very young (∼340 yr) and near (∼3.4 kpc) remnant of a core-collapse supernova. Cas A has been subject to several searches for possible companions, all unsuccessfully. We present new measurements of the proper motions and photometry of stars in the vicinity based on deep HST ACS/WFC and WFC3-IR data. We identify stellar sources that are close enough in projection but using their proper motions we show that none are compatible with being at the location of center at the time of explosion, in agreement with earlier findings. Our photometric measurements allow us to place much deeper (order-of-magnitude) upper limits on the brightness of possible undetected companions. We systematically compare them with model predictions for a wide variety of scenarios. We can confidently rule out the presence of any stellar companion of any reasonable mass and age (main sequence, pre main sequence or stripped) ruling out what many considered to be likely evolutionary scenarios for Type IIb supernova (SN IIb). More exotic scenarios that predict the presence of a compact companion (white dwarf, neutron star or black hole) are still possible as well as scenarios where the progenitor of Cas A was single at the moment of explosion (either because it was truly single, or resulted from a binary that was disrupted, or from a binary merger). The presence of a compact companion would imply that Cas A is of interest to study exotic outcomes of binary evolution. The single-at-death solution would still require fine-tuning of the process that removed most of the envelope through a mass-loss mechanism yet to be identified. We discuss how future constraints from Gaia and even deeper photometric studies may help to place further constraints. article_number: A34 article_processing_charge: No article_type: original author: - first_name: Wolfgang E. full_name: Kerzendorf, Wolfgang E. last_name: Kerzendorf - first_name: Tuan full_name: Do, Tuan last_name: Do - first_name: Selma E. full_name: de Mink, Selma E. last_name: de Mink - 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: Dan full_name: Milisavljevic, Dan last_name: Milisavljevic - first_name: Emmanouil full_name: Zapartas, Emmanouil last_name: Zapartas - first_name: Mathieu full_name: Renzo, Mathieu last_name: Renzo - first_name: Stephen full_name: Justham, Stephen last_name: Justham - first_name: Philipp full_name: Podsiadlowski, Philipp last_name: Podsiadlowski - first_name: Robert A. full_name: Fesen, Robert A. last_name: Fesen citation: ama: Kerzendorf WE, Do T, de Mink SE, et al. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201732206 apa: Kerzendorf, W. E., Do, T., de Mink, S. E., Götberg, Y. L. L., Milisavljevic, D., Zapartas, E., … Fesen, R. A. (2019). No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732206 chicago: Kerzendorf, Wolfgang E., Tuan Do, Selma E. de Mink, Ylva Louise Linsdotter Götberg, Dan Milisavljevic, Emmanouil Zapartas, Mathieu Renzo, Stephen Justham, Philipp Podsiadlowski, and Robert A. Fesen. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201732206. ieee: W. E. Kerzendorf et al., “No surviving non-compact stellar companion to Cassiopeia A,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019. ista: Kerzendorf WE, Do T, de Mink SE, Götberg YLL, Milisavljevic D, Zapartas E, Renzo M, Justham S, Podsiadlowski P, Fesen RA. 2019. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 623, A34. mla: Kerzendorf, Wolfgang E., et al. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics, vol. 623, A34, EDP Sciences, 2019, doi:10.1051/0004-6361/201732206. short: W.E. Kerzendorf, T. Do, S.E. de Mink, Y.L.L. Götberg, D. Milisavljevic, E. Zapartas, M. Renzo, S. Justham, P. Podsiadlowski, R.A. Fesen, Astronomy & Astrophysics 623 (2019). date_created: 2023-08-03T10:14:27Z date_published: 2019-03-27T00:00:00Z date_updated: 2023-08-09T12:28:17Z day: '27' doi: 10.1051/0004-6361/201732206 extern: '1' external_id: arxiv: - '1711.00055' intvolume: ' 623' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201732206 month: '03' 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: No surviving non-compact stellar companion to Cassiopeia A type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 623 year: '2019' ... --- _id: '13468' abstract: - lang: eng text: Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class of explosions observed following the collapse of the core of massive stars. We used analytical estimates and population synthesis simulations to assess the fraction of SNe II progenitors that are expected to have exchanged mass with a companion prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history of mass exchange with a binary companion before exploding. The dominant binary channels leading to SN II progenitors involve the merger of binary stars. Mergers are expected to produce a diversity of SN II progenitor characteristics, depending on the evolutionary timing and properties of the merger. Alternatively, SN II progenitors from interacting binaries may have accreted mass from their companion, and subsequently been ejected from the binary system after their companion exploded. We show that the overall fraction of SN II progenitors that are predicted to have experienced binary interaction is robust against the main physical uncertainties in our models. However, the relative importance of different binary evolutionary channels is affected by changing physical assumptions. We further discuss ways in which binarity might contribute to the observed diversity of SNe II by considering potential observational signatures arising from each binary channel. For supernovae which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb SNe), a surviving non-compact companion would typically indicate that the supernova progenitor star was in a wide, non-interacting binary. We argue that a significant fraction of even Type II-P SNe are expected to have gained mass from a companion prior to explosion. article_number: A5 article_processing_charge: No article_type: original author: - first_name: Emmanouil full_name: Zapartas, Emmanouil last_name: Zapartas - first_name: Selma E. full_name: de Mink, Selma E. last_name: de Mink - first_name: Stephen full_name: Justham, Stephen last_name: Justham - first_name: Nathan full_name: Smith, Nathan last_name: Smith - first_name: Alex full_name: de Koter, Alex last_name: de Koter - first_name: Mathieu full_name: Renzo, Mathieu last_name: Renzo - first_name: Iair full_name: Arcavi, Iair last_name: Arcavi - first_name: Rob full_name: Farmer, Rob last_name: Farmer - 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: Silvia full_name: Toonen, Silvia last_name: Toonen citation: ama: 'Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 2019;631. doi:10.1051/0004-6361/201935854' apa: 'Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo, M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935854' chicago: 'Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith, Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935854.' ieee: 'E. Zapartas et al., “The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction,” Astronomy & Astrophysics, vol. 631. EDP Sciences, 2019.' ista: 'Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I, Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 631, A5.' mla: 'Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics, vol. 631, A5, EDP Sciences, 2019, doi:10.1051/0004-6361/201935854.' short: E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I. Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy & Astrophysics 631 (2019). date_created: 2023-08-03T10:13:52Z date_published: 2019-11-20T00:00:00Z date_updated: 2023-08-09T12:36:09Z day: '20' doi: 10.1051/0004-6361/201935854 extern: '1' external_id: arxiv: - '1907.06687' intvolume: ' 631' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201935854 month: '11' 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: 'The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 631 year: '2019' ... --- _id: '13469' abstract: - lang: eng text: Stars stripped of their envelopes from interaction with a binary companion emit a significant fraction of their radiation as ionizing photons. They are potentially important stellar sources of ionizing radiation, however, they are still often neglected in spectral synthesis simulations or simulations of stellar feedback. In anticipating the large datasets of galaxy spectra from the upcoming James Webb Space Telescope, we modeled the radiative contribution from stripped stars by using detailed evolutionary and spectral models. We estimated their impact on the integrated spectra and specifically on the emission rates of H I-, He I-, and He II-ionizing photons from stellar populations. We find that stripped stars have the largest impact on the ionizing spectrum of a population in which star formation halted several Myr ago. In such stellar populations, stripped stars dominate the emission of ionizing photons, mimicking a younger stellar population in which massive stars are still present. Our models also suggest that stripped stars have harder ionizing spectra than massive stars. The additional ionizing radiation, with which stripped stars contribute affects observable properties that are related to the emission of ionizing photons from stellar populations. In co-eval stellar populations, the ionizing radiation from stripped stars increases the ionization parameter and the production efficiency of hydrogen ionizing photons. They also cause high values for these parameters for about ten times longer than what is predicted for massive stars. The effect on properties related to non-ionizing wavelengths is less pronounced, such as on the ultraviolet continuum slope or stellar contribution to emission lines. However, the hard ionizing radiation from stripped stars likely introduces a characteristic ionization structure of the nebula, which leads to the emission of highly ionized elements such as O2+ and C3+. We, therefore, expect that the presence of stripped stars affects the location in the BPT diagram and the diagnostic ratio of O III to O II nebular emission lines. Our models are publicly available through CDS database and on the STARBURST99 website. article_number: A134 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 - first_name: C. full_name: Leitherer, C. last_name: Leitherer - first_name: C. full_name: Norman, C. last_name: Norman citation: ama: Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 2019;629. doi:10.1051/0004-6361/201834525 apa: Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Leitherer, C., & Norman, C. (2019). The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834525 chicago: Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834525. ieee: Y. L. L. Götberg, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman, “The impact of stars stripped in binaries on the integrated spectra of stellar populations,” Astronomy & Astrophysics, vol. 629. EDP Sciences, 2019. ista: Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. 2019. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 629, A134. mla: Götberg, Ylva Louise Linsdotter, et al. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics, vol. 629, A134, EDP Sciences, 2019, doi:10.1051/0004-6361/201834525. short: Y.L.L. Götberg, S.E. de Mink, J.H. Groh, C. Leitherer, C. Norman, Astronomy & Astrophysics 629 (2019). date_created: 2023-08-03T10:14:00Z date_published: 2019-09-17T00:00:00Z date_updated: 2023-08-09T12:34:11Z day: '17' doi: 10.1051/0004-6361/201834525 extern: '1' external_id: arxiv: - '1908.06102' intvolume: ' 629' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1051/0004-6361/201834525 month: '09' 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: The impact of stars stripped in binaries on the integrated spectra of stellar populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 629 year: '2019' ... --- _id: '9726' abstract: - lang: eng text: A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF) article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: ama: Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001 apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001 chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001. ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019. ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001. mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001. short: M.C. Ucar, R. Lipowsky, (2019). date_created: 2021-07-27T09:51:46Z date_published: 2019-12-19T00:00:00Z date_updated: 2023-08-17T14:07:52Z day: '19' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445.s001 month: '12' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '7166' relation: used_in_publication status: public status: public title: Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '14001' abstract: - lang: eng text: Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses. 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: Daniel full_name: Zindel, Daniel last_name: Zindel - first_name: Vít full_name: Svoboda, Vít last_name: Svoboda - first_name: Elias full_name: Bommeli, Elias last_name: Bommeli - first_name: Manuel full_name: Ochsner, Manuel last_name: Ochsner - first_name: Andres full_name: Tehlar, Andres last_name: Tehlar - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116 apa: Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116 chicago: Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116. ieee: D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019. ista: Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929. mla: Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116. short: D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929. date_created: 2023-08-09T13:10:36Z date_published: 2019-11-13T00:00:00Z date_updated: 2023-08-22T07:40:05Z day: '13' doi: 10.1073/pnas.1907189116 extern: '1' external_id: arxiv: - '1906.10818' pmid: - '31723044' intvolume: ' 116' issue: '48' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1907189116 month: '11' oa: 1 oa_version: Published Version page: 23923-23929 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Real-time probing of chirality during a chemical reaction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2019' ... --- _id: '14002' abstract: - lang: eng text: The advancement of attosecond chronoscopy has made it possible to reveal ultrashort time dynamics of photoionization [1]. Ionization delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect [2], resonances, electron correlations and transport. The extension of this approach to molecules, however, presents great challenges. In addition to the difficulty of identifying correct ionization channels, it is hard to disentangle the role of the anisotropic molecular landscape from the delays inherent to the excitation process itself. Here, we present the measurements of ionization delays from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond streaking spectroscopy, which enables to disentangle the contribution to the delay from the functional ethyl group, being responsible for the characteristic chemical reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes the molecule around the energy of the giant resonance and the released electron is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field, which yields a streaking spectrogram (see figure). Comparative phase analysis of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting overall photoemission delays for ethyl iodide. The data is recorded for multiple photon energies around the iodine 4d resonance and compared to classical Wigner propagation [3] and quantum scattering [4] calculations. Here the outgoing electron, produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby hardly influenced by the molecular potential during the birth process, acquires the necessary information about the influence of the functional ethyl group during its propagation. We find significant delay contributions that can distinguish between different functional groups, providing a sensitive probe of the local molecular environment [5]. This would stimulate to perform further angle resolved measurements in molecules to probe the potential landscape in three dimension. article_number: '8871819' article_processing_charge: No author: - first_name: Shubhadeep full_name: Biswas, Shubhadeep last_name: Biswas - first_name: I. full_name: Liontos, I. last_name: Liontos - first_name: A. M. full_name: Kamal, A. M. last_name: Kamal - first_name: N. G. full_name: Kling, N. G. last_name: Kling - first_name: A. F. full_name: Alharbi, A. F. last_name: Alharbi - first_name: M. full_name: Alharbi, M. last_name: Alharbi - first_name: A. M. full_name: Azzeer, A. M. last_name: Azzeer - first_name: H. J. full_name: Worner, H. J. last_name: Worner - first_name: A. S. full_name: Landsman, A. S. last_name: Landsman - first_name: M. F. full_name: Kling, M. F. last_name: Kling - first_name: B. full_name: Forg, B. last_name: Forg - first_name: J. full_name: Schotz, J. last_name: Schotz - first_name: W. full_name: Schweinberger, W. last_name: Schweinberger - first_name: L. full_name: Ortmann, L. last_name: Ortmann - first_name: T. full_name: Zimmermann, T. last_name: Zimmermann - first_name: L.-W. full_name: Pi, L.-W. last_name: Pi - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: H. A. full_name: Masood, H. A. last_name: Masood citation: ama: 'Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/cleoe-eqec.2019.8871819' apa: 'Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi, M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819' chicago: Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi, M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819. ieee: S. Biswas et al., “Probing molecular influence on photoemission delays,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019. ista: 'Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L, Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: European Conference on Lasers and Electro-Optics, 8871819.' mla: Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/cleoe-eqec.2019.8871819. short: S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger, L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Institute of Electrical and Electronics Engineers, 2019. conference: end_date: 2019-06-27 location: Munich, Germany name: 'CLEO: European Conference on Lasers and Electro-Optics' start_date: 2019-06-23 date_created: 2023-08-09T13:10:49Z date_published: 2019-10-17T00:00:00Z date_updated: 2023-08-22T09:32:56Z day: '17' doi: 10.1109/cleoe-eqec.2019.8871819 extern: '1' language: - iso: eng month: '10' oa_version: None publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference publication_identifier: eisbn: - '9781728104690' isbn: - '9781728104706' publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Probing molecular influence on photoemission delays type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6671' abstract: - lang: eng text: 'In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: André full_name: Lieutier, André last_name: Lieutier - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8 apa: Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8 chicago: Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8. ieee: J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019. ista: Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58. mla: Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8. short: J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58. date_created: 2019-07-24T08:37:29Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-22T12:37:47Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s41468-019-00029-8 ec_funded: 1 file: - access_level: open_access checksum: a5b244db9f751221409cf09c97ee0935 content_type: application/pdf creator: dernst date_created: 2019-07-31T08:09:56Z date_updated: 2020-07-14T12:47:36Z file_id: '6741' file_name: 2019_JournAppliedComputTopol_Boissonnat.pdf file_size: 2215157 relation: main_file file_date_updated: 2020-07-14T12:47:36Z has_accepted_license: '1' intvolume: ' 3' issue: 1-2 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 29–58 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Journal of Applied and Computational Topology publication_identifier: eissn: - 2367-1734 issn: - 2367-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: The reach, metric distortion, geodesic convexity and the variation of tangent spaces 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: 3 year: '2019' ... --- _id: '301' abstract: - lang: eng text: A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense. article_processing_charge: No article_type: original author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: István full_name: Gyöngy, István last_name: Gyöngy citation: ama: Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003 apa: Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003 chicago: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003. ieee: M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019. ista: Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012. mla: Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003. short: M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012. date_created: 2018-12-11T11:45:42Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:20:49Z day: '01' department: - _id: JaMa doi: 10.1016/j.spa.2018.04.003 external_id: arxiv: - '1611.04177' isi: - '000458945300012' intvolume: ' 129' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.04177 month: '03' oa: 1 oa_version: Preprint page: 995-1012 publication: Stochastic Processes and their Applications publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A Feynman–Kac formula for stochastic Dirichlet problems type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 129 year: '2019' ... --- _id: '80' abstract: - lang: eng text: 'We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0 apa: Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0 chicago: Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0. ieee: A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019. ista: Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776. mla: Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0. short: A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776. date_created: 2018-12-11T11:44:31Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-24T14:27:51Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00220-018-3239-0 ec_funded: 1 external_id: isi: - '000467796800007' file: - access_level: open_access checksum: c7e9880b43ac726712c1365e9f2f73a6 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:34:06Z date_updated: 2020-07-14T12:48:07Z file_id: '5688' file_name: 2018_CommunMathPhys_Deuchert.pdf file_size: 893902 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' intvolume: ' 368' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 723-776 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '7974' quality_controlled: '1' scopus_import: '1' status: public title: Bose–Einstein condensation in a dilute, trapped gas at positive temperature 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 368 year: '2019' ... --- _id: '5911' abstract: - lang: eng text: Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved. article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005 apa: Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005 chicago: Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005. ieee: R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019. ista: Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248. mla: Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005. short: R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248. date_created: 2019-02-03T22:59:15Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:29:48Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tree.2018.12.005 ec_funded: 1 external_id: isi: - '000459899000013' file: - access_level: open_access checksum: ef24572d6ebcc1452c067e05410cc4a2 content_type: application/pdf creator: cziletti date_created: 2020-01-09T10:55:58Z date_updated: 2020-07-14T12:47:13Z file_id: '7245' file_name: 2019_Trends_Evolution_Faria.pdf file_size: 1946795 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version page: 239-248 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Trends in Ecology and Evolution publication_identifier: issn: - '01695347' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Evolving inversions 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2019' ... --- _id: '439' abstract: - lang: eng text: "We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system." article_processing_charge: No article_type: original author: - first_name: Tamas full_name: Hausel, Tamas id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Martin full_name: Mereb, Martin id: 43D735EE-F248-11E8-B48F-1D18A9856A87 last_name: Mereb - first_name: Michael full_name: Wong, Michael last_name: Wong citation: ama: Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896 apa: Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896 chicago: Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896. ieee: T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019. ista: Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052. mla: Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896. short: T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052. date_created: 2018-12-11T11:46:29Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-24T14:24:49Z day: '01' department: - _id: TaHa doi: 10.4171/JEMS/896 ec_funded: 1 external_id: arxiv: - '1604.03382' isi: - '000480413600002' intvolume: ' 21' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.03382 month: '10' oa: 1 oa_version: Preprint page: 2995-3052 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Journal of the European Mathematical Society publication_identifier: eissn: - 1435-9855 publication_status: published publisher: European Mathematical Society publist_id: '7384' quality_controlled: '1' scopus_import: '1' status: public title: Arithmetic and representation theory of wild character varieties type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2019' ... --- _id: '105' abstract: - lang: eng text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.' acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.' article_processing_charge: No article_type: original author: - first_name: Ashley full_name: Marsh, Ashley last_name: Marsh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: Lockhart, Paul last_name: Lockhart - first_name: Richard full_name: Leventer, Richard last_name: Leventer citation: ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2 apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2 chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2. ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019. ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166. mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2. short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166. date_created: 2018-12-11T11:44:39Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:28:24Z day: '01' department: - _id: GaNo doi: 10.1038/s41431-018-0231-2 external_id: isi: - '000454111500019' pmid: - '30089829' intvolume: ' 27' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41431-018-0231-2 month: '01' oa: 1 oa_version: Published Version page: 161-166 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Springer Nature publist_id: '7949' quality_controlled: '1' scopus_import: '1' status: public title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2019' ... --- _id: '65' abstract: - lang: eng text: We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2. article_processing_charge: No article_type: original author: - first_name: Konstantinos full_name: Dareiotis, Konstantinos last_name: Dareiotis - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Benjamin full_name: Gess, Benjamin last_name: Gess citation: ama: Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012 apa: Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012 chicago: Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012. ieee: K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019. ista: Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763. mla: Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012. short: K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763. date_created: 2018-12-11T11:44:26Z date_published: 2019-03-05T00:00:00Z date_updated: 2023-08-24T14:30:16Z day: '5' department: - _id: JaMa doi: 10.1016/j.jde.2018.09.012 external_id: arxiv: - '1803.06953' isi: - '000456332500026' intvolume: ' 266' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1803.06953 month: '03' oa: 1 oa_version: Preprint page: 3732-3763 publication: Journal of Differential Equations publication_status: published publisher: Elsevier publist_id: '7989' quality_controlled: '1' scopus_import: '1' status: public title: Entropy solutions for stochastic porous media equations type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 266 year: '2019' ... --- _id: '5907' abstract: - lang: eng text: Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins. article_number: '331' article_processing_charge: No author: - first_name: Réka full_name: Mócsai, Réka last_name: Mócsai - first_name: Rudolf full_name: Figl, Rudolf last_name: Figl - first_name: Clemens full_name: Troschl, Clemens last_name: Troschl - first_name: Richard full_name: Strasser, Richard last_name: Strasser - first_name: Elisabeth full_name: Svehla, Elisabeth last_name: Svehla - first_name: Markus full_name: Windwarder, Markus last_name: Windwarder - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Friedrich full_name: Altmann, Friedrich last_name: Altmann citation: ama: Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1 apa: Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1 chicago: Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1. ieee: R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019. ista: Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331. mla: Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1. short: R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019). date_created: 2019-02-03T22:59:13Z date_published: 2019-01-23T00:00:00Z date_updated: 2023-08-24T14:33:16Z day: '23' ddc: - '580' department: - _id: FlSc doi: 10.1038/s41598-018-36884-1 external_id: isi: - '000456392400012' file: - access_level: open_access checksum: 4129c7d7663d1f8a1edf8c4232372f66 content_type: application/pdf creator: dernst date_created: 2019-02-05T13:10:02Z date_updated: 2020-07-14T12:47:13Z file_id: '5923' file_name: 2019_ScientificReports_Mocsai.pdf file_size: 2124292 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '5908' abstract: - lang: eng text: The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants. article_processing_charge: No article_type: original author: - first_name: Eunkyoung full_name: Lee, Eunkyoung last_name: Lee - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jessica full_name: Pérez-Sancho, Jessica last_name: Pérez-Sancho - first_name: Francisco full_name: Benitez-Fuente, Francisco last_name: Benitez-Fuente - first_name: Matthew full_name: Strelau, Matthew last_name: Strelau - first_name: Alberto P. full_name: Macho, Alberto P. last_name: Macho - first_name: Miguel A. full_name: Botella, Miguel A. last_name: Botella - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Abel full_name: Rosado, Abel last_name: Rosado citation: ama: Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116 apa: Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116 chicago: Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116. ieee: E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019. ista: Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429. mla: Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116. short: E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429. date_created: 2019-02-03T22:59:14Z date_published: 2019-01-22T00:00:00Z date_updated: 2023-08-24T14:31:09Z day: '22' department: - _id: JiFr doi: 10.1073/pnas.1818099116 external_id: isi: - '000456336100050' pmid: - '30610176' intvolume: ' 116' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1818099116 month: '01' oa: 1 oa_version: Published Version page: 1420-1429 pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 116 year: '2019' ... --- _id: '5680' abstract: - lang: eng text: Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones. article_processing_charge: No author: - first_name: Christophe full_name: Andalo, Christophe last_name: Andalo - first_name: Monique full_name: Burrus, Monique last_name: Burrus - first_name: Sandrine full_name: Paute, Sandrine last_name: Paute - first_name: Christine full_name: Lauzeral, Christine last_name: Lauzeral - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142 apa: Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142 chicago: Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142. ieee: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019. ista: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92. mla: Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142. short: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92. date_created: 2018-12-16T22:59:20Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:34:12Z day: '01' department: - _id: NiBa doi: 10.1080/23818107.2018.1545142 external_id: isi: - '000463802800009' intvolume: ' 166' isi: 1 issue: '1' language: - iso: eng month: '01' oa_version: None page: 80-92 publication: Botany Letters publication_identifier: eissn: - '23818115' issn: - '23818107' publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 166 year: '2019' ... --- _id: '5790' abstract: - lang: eng text: The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest. article_processing_charge: No article_type: original author: - first_name: Steven full_name: Chaplick, Steven last_name: Chaplick - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Pavel full_name: Klavík, Pavel last_name: Klavík citation: ama: Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436 apa: Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436 chicago: Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436. ieee: S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019. ista: Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394. mla: Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436. short: S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394. date_created: 2018-12-30T22:59:15Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-24T14:30:43Z day: '01' department: - _id: UlWa doi: 10.1002/jgt.22436 ec_funded: 1 external_id: arxiv: - '1309.2399' isi: - '000485392800004' intvolume: ' 91' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.2399 month: '08' oa: 1 oa_version: Preprint page: 365-394 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Graph Theory publication_identifier: issn: - '03649024' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Extending partial representations of circle graphs type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 91 year: '2019' ... --- _id: '405' abstract: - lang: eng text: We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently. acknowledgement: The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152) article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002 apa: Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002 chicago: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002. ieee: D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019. ista: Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78. mla: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002. short: D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78. date_created: 2018-12-11T11:46:17Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-24T14:31:47Z day: '01' department: - _id: LaEr doi: 10.1016/j.laa.2018.03.002 ec_funded: 1 external_id: arxiv: - '1712.05324' isi: - '000470955300005' intvolume: ' 576' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.05324 month: '09' oa: 1 oa_version: Preprint page: 67-78 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Linear Algebra and Its Applications publication_status: published publisher: Elsevier publist_id: '7424' quality_controlled: '1' scopus_import: '1' status: public title: Jointly convex quantum Jensen divergences type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 576 year: '2019' ... --- _id: '175' abstract: - lang: eng text: An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points. article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Daniel full_name: Loughran, Daniel last_name: Loughran citation: ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514 apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514 chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514. ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019. ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785. mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514. short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785. date_created: 2018-12-11T11:45:01Z date_published: 2019-04-15T00:00:00Z date_updated: 2023-08-24T14:34:56Z day: '15' department: - _id: TiBr doi: 10.1090/tran/7514 external_id: arxiv: - '1705.01999' isi: - '000464034200019' intvolume: ' 371' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.01999 month: '04' oa: 1 oa_version: Preprint page: 5757-5785 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - '10886850' issn: - '00029947' publication_status: published publisher: American Mathematical Society publist_id: '7746' quality_controlled: '1' scopus_import: '1' status: public title: Sieving rational points on varieties type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 371 year: '2019' ... --- _id: '319' abstract: - lang: eng text: We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition. acknowledgement: "MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Martin full_name: Hairer, Martin last_name: Hairer citation: ama: Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1 apa: Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1 chicago: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1. ieee: M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019. ista: Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758. mla: Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1. short: M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758. date_created: 2018-12-11T11:45:48Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-24T14:38:32Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s00440-018-0841-1 external_id: isi: - '000463613800001' file: - access_level: open_access checksum: 288d16ef7291242f485a9660979486e3 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:25:24Z date_updated: 2020-07-14T12:46:03Z file_id: '5722' file_name: 2018_ProbTheory_Gerencser.pdf file_size: 893182 relation: main_file file_date_updated: 2020-07-14T12:46:03Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 697–758 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer publist_id: '7546' quality_controlled: '1' scopus_import: '1' status: public title: Singular SPDEs in domains with boundaries 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 173 year: '2019' ... --- _id: '429' abstract: - lang: eng text: We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent. acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\n" article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019. ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373. mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373. date_created: 2018-12-11T11:46:25Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-24T14:39:00Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00440-018-0835-z ec_funded: 1 external_id: isi: - '000459396500007' file: - access_level: open_access checksum: f9354fa5c71f9edd17132588f0dc7d01 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:12:08Z date_updated: 2020-07-14T12:46:26Z file_id: '5720' file_name: 2018_ProbTheory_Ajanki.pdf file_size: 1201840 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: 1-2 language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 293–373 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: eissn: - '14322064' issn: - '01788051' publication_status: published publisher: Springer publist_id: '7394' quality_controlled: '1' scopus_import: '1' status: public title: Stability of the matrix Dyson equation and random matrices with correlations 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 173 year: '2019' ... --- _id: '5947' abstract: - lang: eng text: Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking. article_processing_charge: No author: - first_name: Bapi full_name: Chatterjee, Bapi id: 3C41A08A-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-2742-4028 - first_name: Sathya full_name: Peri, Sathya last_name: Peri - first_name: Muktikanta full_name: Sa, Muktikanta last_name: Sa - first_name: Nandini full_name: Singhal, Nandini last_name: Singhal citation: ama: 'Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617' apa: 'Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617' chicago: Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617. ieee: B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177. ista: 'Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.' mla: Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617. short: B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177. conference: end_date: 2019-01-07 location: Bangalore, India name: 'ICDCN: Conference on Distributed Computing and Networking' start_date: 2019-01-04 date_created: 2019-02-10T22:59:17Z date_published: 2019-01-04T00:00:00Z date_updated: 2023-08-24T14:41:53Z day: '04' department: - _id: DaAl doi: 10.1145/3288599.3288617 external_id: arxiv: - '1809.00896' isi: - '000484491600019' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.00896 month: '01' oa: 1 oa_version: Preprint page: 168-177 publication: ACM International Conference Proceeding Series publication_identifier: isbn: - '978-1-4503-6094-4 ' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '5857' abstract: - lang: eng text: 'A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: János full_name: Pach, János last_name: Pach citation: ama: 'Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025' apa: 'Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025' chicago: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.' ieee: 'R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.' ista: 'Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231.' mla: 'Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.' short: R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231. date_created: 2019-01-20T22:59:17Z date_published: 2019-04-30T00:00:00Z date_updated: 2023-08-24T14:39:33Z day: '30' department: - _id: UlWa doi: 10.1016/j.dam.2018.12.025 external_id: arxiv: - '1708.08037' isi: - '000466061100020' intvolume: ' 259' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08037 month: '04' oa: 1 oa_version: Preprint page: 266-231 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Discrete Applied Mathematics publication_identifier: issn: - 0166218X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '433' relation: earlier_version status: public scopus_import: '1' status: public title: 'Thrackles: An improved upper bound' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 259 year: '2019' ... --- _id: '5944' abstract: - lang: eng text: Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it. article_number: '9' article_processing_charge: No author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 citation: ama: Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009 apa: Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009 chicago: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009. ieee: B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019. ista: Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9. mla: Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009. short: B. Corominas-Murtra, Life 9 (2019). date_created: 2019-02-10T22:59:15Z date_published: 2019-01-15T00:00:00Z date_updated: 2023-08-24T14:43:41Z day: '15' ddc: - '570' department: - _id: EdHa doi: 10.3390/life9010009 external_id: isi: - '000464125500001' file: - access_level: open_access checksum: 7d2322cd96ace41959909b66702d5cf4 content_type: application/pdf creator: dernst date_created: 2019-02-11T10:45:27Z date_updated: 2020-07-14T12:47:13Z file_id: '5951' file_name: 2019_Life_Corominas.pdf file_size: 963454 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Life publication_identifier: eissn: - '20751729' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Thermodynamics of duplication thresholds in synthetic protocell systems 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '6029' abstract: - lang: eng text: Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy. article_number: '655' article_processing_charge: No author: - first_name: Marco full_name: Lindner, Marco last_name: Lindner - first_name: Aliz full_name: Tresztenyak, Aliz last_name: Tresztenyak - first_name: Gergö full_name: Fülöp, Gergö last_name: Fülöp - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Adrian full_name: Prinz, Adrian last_name: Prinz - first_name: Iris full_name: Prinz, Iris last_name: Prinz - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Gerhard J. full_name: Schütz, Gerhard J. last_name: Schütz - first_name: Eva full_name: Sevcsik, Eva last_name: Sevcsik citation: ama: Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655 apa: Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655 chicago: Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655. ieee: M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019. ista: Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655. mla: Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655. short: M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019). date_created: 2019-02-17T22:59:24Z date_published: 2019-01-24T00:00:00Z date_updated: 2023-08-24T14:45:38Z day: '24' ddc: - '540' department: - _id: JoDa doi: 10.3389/fchem.2018.00655 external_id: isi: - '000456718000001' file: - access_level: open_access checksum: 7841301d7c53b56ef873791b4b6f7b24 content_type: application/pdf creator: dernst date_created: 2019-02-18T15:10:34Z date_updated: 2020-07-14T12:47:17Z file_id: '6039' file_name: 2019_frontiers_Lindner.pdf file_size: 1766820 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Frontiers in Chemistry publication_identifier: eissn: - '22962646' publication_status: published publisher: Frontiers Media S.A. quality_controlled: '1' scopus_import: '1' status: public title: A fast and simple contact printing approach to generate 2D protein nanopatterns 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2019' ... --- _id: '6028' abstract: - lang: eng text: We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small. article_processing_charge: Yes (via OA deal) author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Martin full_name: Hairer, Martin last_name: Hairer citation: ama: Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816 apa: Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816 chicago: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816. ieee: M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019. ista: Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005. mla: Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816. short: M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005. date_created: 2019-02-17T22:59:24Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-08-24T14:44:31Z day: '08' ddc: - '500' department: - _id: JaMa doi: 10.1002/cpa.21816 external_id: isi: - '000475465000003' file: - access_level: open_access checksum: 09aec427eb48c0f96a1cce9ff53f013b content_type: application/pdf creator: kschuh date_created: 2020-01-07T13:25:55Z date_updated: 2020-07-14T12:47:17Z file_id: '7237' file_name: 2019_Wiley_Gerencser.pdf file_size: 381350 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 72' isi: 1 issue: '9' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1983-2005 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A solution theory for quasilinear singular SPDEs 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 72 year: '2019' ... --- _id: '5948' abstract: - lang: eng text: We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: International Conference on Verification, Model Checking, and Abstract Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22' apa: 'Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In International Conference on Verification, Model Checking, and Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-11245-5_22' chicago: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In International Conference on Verification, Model Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-11245-5_22. ieee: H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in International Conference on Verification, Model Checking, and Abstract Interpretation, Cascais, Portugal, 2019, vol. 11388, pp. 468–490. ista: 'Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490.' mla: Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” International Conference on Verification, Model Checking, and Abstract Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22. short: H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490. conference: end_date: 2019-01-15 location: Cascais, Portugal name: 'VMCAI: Verification, Model Checking, and Abstract Interpretation' start_date: 2019-01-13 date_created: 2019-02-10T22:59:17Z date_published: 2019-01-11T00:00:00Z date_updated: 2023-08-24T14:42:22Z day: '11' department: - _id: KrCh doi: 10.1007/978-3-030-11245-5_22 external_id: arxiv: - '1701.02944' isi: - '000931943000022' intvolume: ' 11388' isi: 1 language: - iso: eng main_file_link: - url: https://arxiv.org/abs/1701.02944 month: '01' oa_version: Preprint page: 468-490 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: International Conference on Verification, Model Checking, and Abstract Interpretation publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Termination of nondeterministic probabilistic programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11388 year: '2019' ... --- _id: '5945' abstract: - lang: eng text: In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy. article_processing_charge: No article_type: original author: - first_name: Mariela D. full_name: Petkova, Mariela D. last_name: Petkova - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Eric F. full_name: Wieschaus, Eric F. last_name: Wieschaus - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007 apa: Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007 chicago: Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007. ieee: M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019. ista: Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15. mla: Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007. short: M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15. date_created: 2019-02-10T22:59:16Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:42:47Z day: '07' department: - _id: GaTk doi: 10.1016/j.cell.2019.01.007 external_id: isi: - '000457969200015' pmid: - '30712870' intvolume: ' 176' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2019.01.007 month: '02' oa: 1 oa_version: Published Version page: 844-855.e15 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Cell publication_status: published publisher: Cell Press quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/ scopus_import: '1' status: public title: Optimal decoding of cellular identities in a genetic network type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 176 year: '2019' ... --- _id: '5943' abstract: - lang: eng text: The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour. article_processing_charge: No article_type: original author: - first_name: Lukasz full_name: Klotz, Lukasz id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87 last_name: Klotz orcid: 0000-0003-1740-7635 - first_name: Konrad full_name: Gumowski, Konrad last_name: Gumowski - first_name: José Eduardo full_name: Wesfreid, José Eduardo last_name: Wesfreid citation: ama: Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974 apa: Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974 chicago: Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974. ieee: L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019. ista: Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406. mla: Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974. short: L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406. date_created: 2019-02-10T22:59:15Z date_published: 2019-03-25T00:00:00Z date_updated: 2023-08-24T14:43:13Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2018.974 ec_funded: 1 external_id: arxiv: - '1902.07931' isi: - '000526029100016' intvolume: ' 863' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07931 month: '03' oa: 1 oa_version: Preprint page: 386-406 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: Experiments on a jet in a crossflow in the low-velocity-ratio regime type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 863 year: '2019' ... --- _id: '6042' abstract: - lang: eng text: Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques. alternative_title: - LNCS article_processing_charge: No author: - first_name: Maria full_name: Christakis, Maria last_name: Christakis - first_name: Matthias full_name: Heizmann, Matthias last_name: Heizmann - first_name: Muhammad Numair full_name: Mansur, Muhammad Numair last_name: Mansur - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Valentin full_name: Wüstholz, Valentin last_name: Wüstholz citation: ama: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13' apa: 'Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13' chicago: Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13. ieee: M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243. ista: 'Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.' mla: Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13. short: M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243. conference: end_date: 2019-04-11 location: Prague, Czech Republic name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2019-04-06 date_created: 2019-02-18T16:44:06Z date_published: 2019-04-04T00:00:00Z date_updated: 2023-08-24T14:47:45Z day: '04' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-17462-0_13 ec_funded: 1 external_id: isi: - '000681166500013' file: - access_level: open_access checksum: 9998496f6fe202c0a19124b4209154c6 content_type: application/pdf creator: dernst date_created: 2019-05-10T14:16:05Z date_updated: 2020-07-14T12:47:17Z file_id: '6408' file_name: 2019_LNCS_Christakis.pdf file_size: 773083 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 11427' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 226-243 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _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: '25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Semantic fault localization and suspiciousness ranking 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11427 year: '2019' ... --- _id: '6035' abstract: - lang: eng text: 'We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.' article_processing_charge: No author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Kostiantyn full_name: Potomkin, Kostiantyn last_name: Potomkin - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804' apa: 'Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804' chicago: 'Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.' ieee: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.' ista: 'Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control vol. 22, 39–44.' mla: 'Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.' short: 'S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.' conference: end_date: 2019-04-18 location: Montreal, QC, Canada name: 'HSCC: Hybrid Systems Computation and Control' start_date: 2019-04-16 date_created: 2019-02-18T14:43:28Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-08-24T14:47:21Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1145/3302504.3311804 ec_funded: 1 external_id: arxiv: - '1901.10736' isi: - '000516713900005' file: - access_level: open_access checksum: 28ed56439aea5991c3122d4730fd828f content_type: application/pdf creator: cschilli date_created: 2019-03-05T09:27:18Z date_updated: 2020-07-14T12:47:17Z file_id: '6067' file_name: hscc19.pdf file_size: 3784414 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 22' isi: 1 keyword: - reachability analysis - hybrid systems - lazy computation language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 39-44 project: - _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 - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - '9781450362825' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: 'JuliaReach: A toolbox for set-based reachability' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2019' ... --- _id: '6052' abstract: - lang: eng text: 'Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.' article_processing_charge: No article_type: original author: - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Silvio O full_name: Rizzoli, Silvio O last_name: Rizzoli - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3 apa: Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3 chicago: Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3. ieee: S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019. ista: Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863. mla: Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3. short: S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863. date_created: 2019-02-24T22:59:20Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:48:33Z day: '01' ddc: - '570' department: - _id: JoDa - _id: Bio doi: 10.1038/s41596-018-0117-3 ec_funded: 1 external_id: isi: - '000459890700008' pmid: - '30778205' file: - access_level: open_access checksum: 7efb9951e7ddf3e3dcc2fb92b859c623 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: kschuh date_created: 2021-06-29T14:41:46Z date_updated: 2021-06-29T14:41:46Z file_id: '9619' file_name: 181031_Truckenbrodt_ExM_NatProtoc.docx file_size: 84478958 relation: main_file success: 1 file_date_updated: 2021-06-29T14:41:46Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 832–863 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules publication: Nature Protocols publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: A practical guide to optimization in X10 expansion microscopy type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2019' ... --- _id: '6025' abstract: - lang: eng text: Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation. acknowledged_ssus: - _id: Bio - _id: LifeSc article_number: e42093 article_processing_charge: No author: - first_name: Daniel full_name: Capek, Daniel id: 31C42484-F248-11E8-B48F-1D18A9856A87 last_name: Capek orcid: 0000-0001-5199-9940 - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Alexandra Madelaine full_name: Tichy, Alexandra Madelaine last_name: Tichy - first_name: Maurizio full_name: Morri, Maurizio id: 4863116E-F248-11E8-B48F-1D18A9856A87 last_name: Morri - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 2019;8. doi:10.7554/eLife.42093 apa: Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., & Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42093 chicago: Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42093. ieee: D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093. mla: Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” ELife, vol. 8, e42093, eLife Sciences Publications, 2019, doi:10.7554/eLife.42093. short: D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019). date_created: 2019-02-17T22:59:22Z date_published: 2019-02-06T00:00:00Z date_updated: 2023-08-24T14:46:01Z day: '06' ddc: - '570' department: - _id: CaHe - _id: HaJa doi: 10.7554/eLife.42093 ec_funded: 1 external_id: isi: - '000458025300001' file: - access_level: open_access checksum: 6cb4ca6d4aa96f6f187a5983aa3e660a content_type: application/pdf creator: dernst date_created: 2019-02-18T15:17:21Z date_updated: 2020-07-14T12:47:17Z file_id: '6041' file_name: 2019_elife_Capek.pdf file_size: 5500707 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication: eLife publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2019' ... --- _id: '6022' abstract: - lang: eng text: The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation. article_number: e2005902 article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902. ieee: R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902. mla: Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019). date_created: 2019-02-17T22:59:21Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902 external_id: isi: - '000460317100001' file: - access_level: open_access checksum: 5f34001617ee729314ca520c049b1112 content_type: application/pdf creator: dernst date_created: 2019-02-18T14:57:24Z date_updated: 2020-07-14T12:47:17Z file_id: '6036' file_name: 2019_PLOS_Merrill.pdf file_size: 2005949 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9801' relation: research_data status: public scopus_import: '1' status: public title: Genetic dissection of assortative mating behavior tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2019' ... --- _id: '6023' abstract: - lang: eng text: Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain. article_processing_charge: No author: - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Alja full_name: Van Der Schuren, Alja last_name: Van Der Schuren - first_name: Maritza full_name: Van Dop, Maritza last_name: Van Dop - first_name: Luc full_name: Van Galen, Luc last_name: Van Galen - first_name: Shunsuke full_name: Saiga, Shunsuke last_name: Saiga - first_name: Milad full_name: Adibi, Milad last_name: Adibi - first_name: Barbara full_name: Möller, Barbara last_name: Möller - first_name: Colette A. full_name: Ten Hove, Colette A. last_name: Ten Hove - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Richard full_name: Smith, Richard last_name: Smith - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6 apa: Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6 chicago: Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6. ieee: S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019. ista: Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166. mla: Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6. short: S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166. date_created: 2019-02-17T22:59:21Z date_published: 2019-02-08T00:00:00Z date_updated: 2023-08-24T14:46:47Z day: '08' department: - _id: JiFr - _id: EvBe doi: 10.1038/s41477-019-0363-6 ec_funded: 1 external_id: isi: - '000460479600014' intvolume: ' 5' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/479113v1.abstract month: '02' oa: 1 oa_version: Submitted Version page: 160-166 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Plants publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2019' ... --- _id: '6053' abstract: - lang: eng text: Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information. article_processing_charge: No article_type: original author: - first_name: Mahmoud full_name: Kalaee, Mahmoud last_name: Kalaee - first_name: Mohammad full_name: Mirhosseini, Mohammad last_name: Mirhosseini - first_name: Paul B. full_name: Dieterle, Paul B. last_name: Dieterle - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Oskar full_name: Painter, Oskar last_name: Painter citation: ama: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2 apa: Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2 chicago: Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2. ieee: M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019. ista: Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339. mla: Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2. short: M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339. date_created: 2019-02-24T22:59:21Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-24T14:48:08Z day: '01' department: - _id: JoFi doi: 10.1038/s41565-019-0377-2 external_id: isi: - '000463195700014' intvolume: ' 14' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://authors.library.caltech.edu/92123/ month: '04' oa: 1 oa_version: Submitted Version page: 334–339 publication: Nature Nanotechnology publication_identifier: eissn: - 1748-3395 issn: - 1748-3387 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantum electromechanics of a hypersonic crystal type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2019' ... --- _id: '6050' abstract: - lang: eng text: 'We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. ' article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Roman full_name: Fedorov, Roman last_name: Fedorov citation: ama: Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240 apa: Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240 chicago: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240. ieee: A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019. ista: Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102. mla: Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240. short: A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102. date_created: 2019-02-24T22:59:19Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:48:59Z day: '01' department: - _id: HeEd doi: 10.1090/proc/14240 external_id: arxiv: - '1709.02562' isi: - '000450363900008' intvolume: ' 147' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.02562 month: '01' oa: 1 oa_version: Preprint page: 91-102 publication: Proceedings of the American Mathematical Society publication_status: published publisher: AMS quality_controlled: '1' scopus_import: '1' status: public title: Two circles and only a straightedge type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 147 year: '2019' ... --- _id: '9801' article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006. ieee: R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006. mla: Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019). date_created: 2021-08-06T11:34:56Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902.s006 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6022' relation: used_in_publication status: public status: public title: Raw behavioral data type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6095' abstract: - lang: eng text: Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. article_processing_charge: No author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Pragya full_name: Chaube, Pragya last_name: Chaube - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Tomas full_name: Larsson, Tomas last_name: Larsson - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: Emily M. full_name: Lemmon, Emily M. last_name: Lemmon - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Marina full_name: Panova, Marina last_name: Panova - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972 apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972 chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972. ieee: R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019. ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393. mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972. short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393. date_created: 2019-03-10T22:59:21Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:50:27Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.14972 external_id: isi: - '000465219200013' file: - access_level: open_access checksum: f915885756057ec0ca5912a41f46a887 content_type: application/pdf creator: dernst date_created: 2019-03-11T16:12:54Z date_updated: 2020-07-14T12:47:19Z file_id: '6097' file_name: 2019_MolecularEcology_Faria.pdf file_size: 1510715 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1375-1393 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9837' relation: research_data status: public scopus_import: '1' status: public title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 28 year: '2019' ...