[{"title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","abstract":[{"text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["37666965"],"isi":["001069238800014"]},"page":"1500-1513","article_processing_charge":"Yes (in subscription journal)","pmid":1,"volume":9,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"S","last_name":"Roychoudhry","full_name":"Roychoudhry, S"},{"last_name":"Sageman-Furnas","first_name":"K","full_name":"Sageman-Furnas, K"},{"full_name":"Wolverton, C","last_name":"Wolverton","first_name":"C"},{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gergely","last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Angelis, M","last_name":"De Angelis","first_name":"M"},{"last_name":"Goodman","first_name":"HL","full_name":"Goodman, HL"},{"first_name":"N","last_name":"Capstaff","full_name":"Capstaff, N"},{"full_name":"JPB, Lloyd","first_name":"Lloyd","last_name":"JPB"},{"full_name":"Mullen, J","last_name":"Mullen","first_name":"J"},{"full_name":"Hangarter, R","last_name":"Hangarter","first_name":"R"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Kepinski, S","first_name":"S","last_name":"Kepinski"}],"ddc":["580"],"has_accepted_license":"1","file":[{"relation":"main_file","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","access_level":"open_access","date_updated":"2023-09-20T10:51:31Z","file_size":9647103,"file_id":"14351","creator":"dernst","success":1,"date_created":"2023-09-20T10:51:31Z","file_name":"2023_NaturePlants_Roychoudhry.pdf","content_type":"application/pdf"}],"quality_controlled":"1","publication":"Nature Plants","doi":"10.1038/s41477-023-01478-x","publication_identifier":{"issn":["2055-0278"]},"year":"2023","date_created":"2023-09-15T09:56:01Z","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","date_updated":"2024-10-21T06:01:33Z","language":[{"iso":"eng"}],"month":"09","date_published":"2023-09-01T00:00:00Z","oa":1,"file_date_updated":"2023-09-20T10:51:31Z","isi":1,"_id":"14339","scopus_import":"1","type":"journal_article","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","article_type":"original","oa_version":"Published Version","intvolume":"         9","citation":{"mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>.","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513.","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. 2023;9:1500-1513. doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>","ieee":"S. Roychoudhry <i>et al.</i>, “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” <i>Nature Plants</i>, vol. 9. Springer Nature, pp. 1500–1513, 2023.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513."},"status":"public","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"year":"2023","date_created":"2023-09-17T22:01:09Z","publication":"Nature","issue":"7977","doi":"10.1038/s41586-023-06399-5","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"quality_controlled":"1","file":[{"relation":"main_file","checksum":"9c9f172ba0a9a301d76fff4229812464","access_level":"open_access","file_size":3247252,"date_updated":"2024-06-04T09:24:34Z","file_id":"17118","creator":"dernst","success":1,"date_created":"2024-06-04T09:24:34Z","file_name":"2023_submittedversion.pdf","content_type":"application/pdf"}],"corr_author":"1","ddc":["530"],"has_accepted_license":"1","volume":621,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","last_name":"Lopez Alonso"},{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"}],"related_material":{"link":[{"relation":"press_release","url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","description":"News on ISTA website"}]},"pmid":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"abstract":[{"text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines.","lang":"eng"}],"external_id":{"isi":["001168947700009"],"pmid":["37673988"]},"publication_status":"published","page":"71-74","article_processing_charge":"No","title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","status":"public","day":"07","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"},{"grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow in complex fluids","call_identifier":"FWF"}],"citation":{"chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., &#38; Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>.","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” <i>Nature</i>, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. 2023;621(7977):71-74. doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74."},"type":"journal_article","acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","article_type":"original","oa_version":"Submitted Version","intvolume":"       621","_id":"14341","scopus_import":"1","oa":1,"file_date_updated":"2024-06-04T09:24:34Z","isi":1,"publisher":"Springer Nature","department":[{"_id":"BjHo"}],"date_updated":"2025-09-09T12:59:04Z","month":"09","language":[{"iso":"eng"}],"date_published":"2023-09-07T00:00:00Z"},{"ddc":["530"],"has_accepted_license":"1","file":[{"date_updated":"2023-09-20T11:36:16Z","file_size":1486715,"relation":"main_file","checksum":"89a1b604d58b209fec66c6b6f919ac98","access_level":"open_access","file_id":"14353","creator":"dernst","success":1,"file_name":"2023_ApplPhysLetter_Lorenc.pdf","content_type":"application/pdf","date_created":"2023-09-20T11:36:16Z"}],"quality_controlled":"1","corr_author":"1","publication":"Applied Physics Letters","issue":"9","publication_identifier":{"issn":["0003-6951"]},"doi":"10.1063/5.0161713","article_number":"091104","year":"2023","date_created":"2023-09-17T22:01:09Z","title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","abstract":[{"text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.","lang":"eng"}],"external_id":{"isi":["001145465400004"],"arxiv":["2306.09043"]},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","volume":123,"author":[{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Lorenc, D., &#38; Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>.","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>.","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” <i>Applied Physics Letters</i>, vol. 123, no. 9. AIP Publishing, 2023.","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. 2023;123(9). doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>","ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104."},"status":"public","day":"28","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"ZhAl"}],"arxiv":1,"publisher":"AIP Publishing","date_updated":"2025-09-09T12:58:23Z","language":[{"iso":"eng"}],"month":"08","date_published":"2023-08-28T00:00:00Z","oa":1,"file_date_updated":"2023-09-20T11:36:16Z","isi":1,"_id":"14342","scopus_import":"1","type":"journal_article","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","article_type":"original","oa_version":"Published Version","intvolume":"       123"},{"volume":2023,"author":[{"first_name":"Michael","last_name":"Anastos","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","full_name":"Anastos, Michael"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","publication_status":"published","external_id":{"arxiv":["2111.14759"]},"abstract":[{"lang":"eng","text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and  respectively, each being best possible in its own setting."}],"article_processing_charge":"No","page":"2286-2323","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","doi":"10.1137/1.9781611977554.ch88","publication_identifier":{"isbn":["9781611977554"]},"date_created":"2023-09-17T22:01:10Z","year":"2023","conference":{"start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms","location":"Florence, Italy","end_date":"2023-01-25"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.14759","open_access":"1"}],"quality_controlled":"1","corr_author":"1","scopus_import":"1","_id":"14344","type":"conference","oa_version":"Preprint","intvolume":"      2023","date_updated":"2024-10-09T21:07:01Z","department":[{"_id":"MaKw"}],"arxiv":1,"publisher":"Society for Industrial and Applied Mathematics","date_published":"2023-01-01T00:00:00Z","month":"01","language":[{"iso":"eng"}],"oa":1,"status":"public","day":"01","citation":{"short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, vol. 2023, pp. 2286–2323.","ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>","chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>."}},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael"},{"first_name":"Isabelle D","last_name":"Mayer","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","full_name":"Mayer, Isabelle D"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"volume":14,"title":"Synchronization in collectively moving inanimate and living active matter","article_processing_charge":"Yes","abstract":[{"text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-41432-1","publication":"Nature Communications","year":"2023","date_created":"2023-09-24T22:01:10Z","article_number":"5633","has_accepted_license":"1","ddc":["530","570"],"corr_author":"1","file":[{"relation":"main_file","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","access_level":"open_access","file_size":2317272,"date_updated":"2023-09-25T08:32:37Z","file_id":"14366","creator":"dernst","success":1,"date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","content_type":"application/pdf"}],"quality_controlled":"1","_id":"14361","scopus_import":"1","article_type":"original","intvolume":"        14","oa_version":"Published Version","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","type":"journal_article","month":"09","language":[{"iso":"eng"}],"date_published":"2023-09-13T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"date_updated":"2025-04-14T13:10:03Z","isi":1,"oa":1,"file_date_updated":"2023-09-25T08:32:37Z","status":"public","day":"13","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>."},"project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"},{"name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}]},{"article_number":"114129","date_created":"2023-09-24T22:01:11Z","year":"2023","publication":"Theoretical Computer Science","doi":"10.1016/j.tcs.2023.114129","publication_identifier":{"issn":["0304-3975"]},"quality_controlled":"1","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.08424 "}],"volume":977,"author":[{"full_name":"Castellano, Ilaria","first_name":"Ilaria","last_name":"Castellano"},{"full_name":"Giordano Bruno, Anna","first_name":"Anna","last_name":"Giordano Bruno"},{"first_name":"Nicolò","last_name":"Zava","orcid":"0000-0001-8686-1888","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","full_name":"Zava, Nicolò"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2212.08424"],"isi":["001076934000001"]},"publication_status":"published","abstract":[{"text":"Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy.","lang":"eng"}],"article_processing_charge":"No","title":"Weakly weighted generalised quasi-metric spaces and semilattices","status":"public","day":"25","citation":{"apa":"Castellano, I., Giordano Bruno, A., &#38; Zava, N. (2023). Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>","chicago":"Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>.","mla":"Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>, vol. 977, 114129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>.","short":"I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023).","ieee":"I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised quasi-metric spaces and semilattices,” <i>Theoretical Computer Science</i>, vol. 977. Elsevier, 2023.","ama":"Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. 2023;977. doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>","ista":"Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129."},"type":"journal_article","oa_version":"Preprint","intvolume":"       977","article_type":"original","scopus_import":"1","_id":"14362","oa":1,"isi":1,"date_updated":"2024-10-09T21:07:00Z","publisher":"Elsevier","arxiv":1,"department":[{"_id":"HeEd"}],"date_published":"2023-10-25T00:00:00Z","language":[{"iso":"eng"}],"month":"10"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","first_name":"Gloria","last_name":"Colombo"},{"first_name":"Florianne E","last_name":"Schoot Uiterkamp","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E"},{"last_name":"Sternberg","first_name":"Felix","full_name":"Sternberg, Felix"},{"orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino"},{"last_name":"Pohl","first_name":"Elena E.","full_name":"Pohl, Elena E."},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert"}],"volume":26,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"pmid":1,"article_processing_charge":"Yes","publication_status":"published","external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","date_created":"2023-09-24T22:01:11Z","year":"2023","article_number":"107780","publication_identifier":{"eissn":["2589-0042"]},"doi":"10.1016/j.isci.2023.107780","issue":"10","publication":"iScience","corr_author":"1","quality_controlled":"1","file":[{"date_updated":"2023-11-07T08:53:21Z","file_size":8197935,"access_level":"open_access","relation":"main_file","checksum":"be1a560efdd96d20712311f4fc54aac2","file_id":"14497","success":1,"creator":"dernst","file_name":"2023_iScience_Maes.pdf","content_type":"application/pdf","date_created":"2023-11-07T08:53:21Z"}],"has_accepted_license":"1","ddc":["570"],"intvolume":"        26","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","scopus_import":"1","_id":"14363","isi":1,"file_date_updated":"2023-11-07T08:53:21Z","oa":1,"date_published":"2023-10-20T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2024-10-09T21:07:01Z","publisher":"Elsevier","department":[{"_id":"SaSi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"20","status":"public","citation":{"mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>, vol. 26, no. 10, 107780, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>.","apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., &#38; Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>iScience</i>. 2023;26(10). doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","ieee":"M. E. Maes <i>et al.</i>, “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” <i>iScience</i>, vol. 26, no. 10. Elsevier, 2023.","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023)."}},{"related_material":{"record":[{"status":"public","id":"6676","relation":"earlier_version"}]},"volume":52,"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Zhu, Leqi","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5","first_name":"Leqi","last_name":"Zhu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Why extension-based proofs fail","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among  processes or approximate agreement on a cycle of length 4 among  processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power.","lang":"eng"}],"external_id":{"isi":["001082972300004"],"arxiv":["1811.01421"]},"publication_status":"published","page":"913-944","article_processing_charge":"No","publication":"SIAM Journal on Computing","issue":"4","doi":"10.1137/20M1375851","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"year":"2023","date_created":"2023-09-24T22:01:11Z","main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"quality_controlled":"1","_id":"14364","scopus_import":"1","acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","type":"journal_article","article_type":"original","intvolume":"        52","oa_version":"Preprint","publisher":"Society for Industrial and Applied Mathematics","arxiv":1,"department":[{"_id":"DaAl"}],"date_updated":"2025-05-14T11:26:06Z","month":"07","language":[{"iso":"eng"}],"date_published":"2023-07-25T00:00:00Z","oa":1,"isi":1,"day":"25","status":"public","ec_funded":1,"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2023). Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. 2023;52(4):913-944. doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” <i>SIAM Journal on Computing</i>, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023."}},{"_id":"14374","oa_version":"Published Version","type":"dissertation","month":"09","language":[{"iso":"eng"}],"date_published":"2023-09-30T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_updated":"2026-04-07T13:27:39Z","oa":1,"file_date_updated":"2023-10-06T11:38:01Z","alternative_title":["ISTA Thesis"],"day":"30","status":"public","ec_funded":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"citation":{"ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","mla":"Roos, Barbara. <i>Boundary Superconductivity in BCS Theory</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>.","apa":"Roos, B. (2023). <i>Boundary superconductivity in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>"},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"related_material":{"record":[{"status":"public","id":"10850","relation":"part_of_dissertation"},{"id":"13207","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Roos, Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","first_name":"Barbara","last_name":"Roos"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","title":"Boundary superconductivity in BCS theory","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"page":"206","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap  in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space."}],"publication_status":"published","doi":"10.15479/at:ista:14374","publication_identifier":{"issn":["2663-337X"]},"year":"2023","date_created":"2023-09-28T14:23:04Z","has_accepted_license":"1","ddc":["515","539"],"corr_author":"1","file":[{"date_created":"2023-10-06T11:35:56Z","content_type":"application/pdf","file_name":"phd-thesis-draft_pdfa_acrobat.pdf","creator":"broos","file_id":"14398","checksum":"ef039ffc3de2cb8dee5b14110938e9b6","relation":"main_file","access_level":"open_access","file_size":2365702,"date_updated":"2023-10-06T11:35:56Z"},{"date_created":"2023-10-06T11:38:01Z","content_type":"application/x-zip-compressed","file_name":"Version5.zip","creator":"broos","file_id":"14399","relation":"source_file","checksum":"81dcac33daeefaf0111db52f41bb1fd0","access_level":"closed","date_updated":"2023-10-06T11:38:01Z","file_size":4691734}]},{"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","publication_status":"published","external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"abstract":[{"text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.","lang":"eng"}],"article_processing_charge":"Yes","pmid":1,"volume":14,"author":[{"last_name":"Ucar","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Emmi","last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi"},{"first_name":"Inam","last_name":"Liaqat","full_name":"Liaqat, Inam"},{"full_name":"Jakobsson, Emma","first_name":"Emma","last_name":"Jakobsson"},{"full_name":"Nurmi, Harri","last_name":"Nurmi","first_name":"Harri"},{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","first_name":"Kari"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"checksum":"4fe5423403f2531753bcd9e0fea48e05","relation":"main_file","access_level":"open_access","date_updated":"2023-10-03T07:46:36Z","file_size":8143264,"file_id":"14384","creator":"dernst","success":1,"date_created":"2023-10-03T07:46:36Z","content_type":"application/pdf","file_name":"2023_NatureComm_Ucar.pdf"}],"corr_author":"1","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-41456-7","article_number":"5878","date_created":"2023-10-01T22:01:13Z","year":"2023","date_updated":"2025-04-14T07:43:56Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","date_published":"2023-09-21T00:00:00Z","language":[{"iso":"eng"}],"month":"09","file_date_updated":"2023-10-03T07:46:36Z","oa":1,"isi":1,"scopus_import":"1","_id":"14378","type":"journal_article","acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","intvolume":"        14","oa_version":"Published Version","article_type":"original","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"citation":{"mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>, vol. 14, 5878, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., &#38; Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>.","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>","short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","ieee":"M. C. Ucar <i>et al.</i>, “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"status":"public","day":"21","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1},{"publication":"Synthetic Metals","doi":"10.1016/j.synthmet.2023.117463","publication_identifier":{"issn":["0379-6779"]},"article_number":"117463","year":"2023","date_created":"2023-10-01T22:01:13Z","quality_controlled":"1","volume":299,"author":[{"full_name":"Mahato, Neelima","last_name":"Mahato","first_name":"Neelima"},{"full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","first_name":"Saurabh","last_name":"Singh"},{"last_name":"Faisal","first_name":"Mohammad","full_name":"Faisal, Mohammad"},{"full_name":"Sreekanth, T. V.M.","first_name":"T. V.M.","last_name":"Sreekanth"},{"full_name":"Majumder, Sutripto","first_name":"Sutripto","last_name":"Majumder"},{"first_name":"Kisoo","last_name":"Yoo","full_name":"Yoo, Kisoo"},{"last_name":"Kim","first_name":"Jonghoon","full_name":"Kim, Jonghoon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite","abstract":[{"text":"We report on a simple surfactant/template free chemical route for the synthesis of semi-polycrystalline polyaniline-graphite (SPani-graphite) composite and its application as an electroactive material in electrochemical charge storage. The synthesized material exhibits well-defined poly-crystallographic lattices in high resolution transmission electron micrographs and sharp peaks in x-ray diffraction spectra suggesting crystalline nature of the material. The specific capacitance computed from the galvanostatic charge-discharge (GCD) data obtained from 3-electrode cell configuration using 1 M aq. Na2SO4 as an electrolyte was 111.4 F g−1 at a current density of 0.1 A g−1 which rises to 269 F g−1 at an elevated current density of 1.0 A g−1. A similar pattern of increase in the specific capacitance values with an increase in the current density was observed in the results obtained from 2-electrode symmetric device configuration using polymer gel electrolyte (xanthan gum in 1 M aq. Na2SO4). The specific capacitance computed from the GCD data obtained from the device configuration was 20 F g−1 at the current density of 1.0 A g−1. The device delivers an energy density of 1.7 Wh kg−1 and a power density of 2.48 kWh kg−1 at an applied current density of 0.5 A g−1 suggesting an excellent rate capability and power management. In addition, the device exhibits ⁓92 % specific capacitance retention up to 8000 continuous GCD cycles and ⁓80 % coulombic efficiency up to 10,000 continuous GCD cycles indicating excellent cycling stability. The unique feature of increasing specific capacitance with respect to applied current density is attributed to the presence of semi-polycrystalline phases in the SPani-graphite matrix. The material behaves as a surface redox supercapacitor and its unique mechanism of charge storage is discussed in detail in the article.","lang":"eng"}],"external_id":{"isi":["001083568900001"]},"publication_status":"published","article_processing_charge":"No","status":"public","day":"01","citation":{"short":"N. Mahato, S. Singh, M. Faisal, T.V.M. Sreekanth, S. Majumder, K. Yoo, J. Kim, Synthetic Metals 299 (2023).","ieee":"N. Mahato <i>et al.</i>, “Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite,” <i>Synthetic Metals</i>, vol. 299. Elsevier, 2023.","ista":"Mahato N, Singh S, Faisal M, Sreekanth TVM, Majumder S, Yoo K, Kim J. 2023. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. Synthetic Metals. 299, 117463.","ama":"Mahato N, Singh S, Faisal M, et al. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. 2023;299. doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>","apa":"Mahato, N., Singh, S., Faisal, M., Sreekanth, T. V. M., Majumder, S., Yoo, K., &#38; Kim, J. (2023). Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>","chicago":"Mahato, Neelima, Saurabh Singh, Mohammad Faisal, T. V.M. Sreekanth, Sutripto Majumder, Kisoo Yoo, and Jonghoon Kim. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>.","mla":"Mahato, Neelima, et al. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>, vol. 299, 117463, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>."},"_id":"14379","scopus_import":"1","acknowledgement":"This work was supported by 2023 Yeungnam University Research Grant.","type":"journal_article","article_type":"original","intvolume":"       299","oa_version":"None","publisher":"Elsevier","department":[{"_id":"MaIb"}],"date_updated":"2024-01-30T13:55:50Z","language":[{"iso":"eng"}],"month":"11","date_published":"2023-11-01T00:00:00Z","isi":1},{"citation":{"apa":"Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., &#38; Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>","chicago":"Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola, Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>.","mla":"Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>, vol. 18, 67, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>.","short":"M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells, Molecular Neurodegeneration 18 (2023).","ieee":"M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R. W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps,” <i>Molecular Neurodegeneration</i>, vol. 18. Springer Nature, 2023.","ista":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. 18, 67.","ama":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. 2023;18. doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>"},"day":"26","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"09","date_published":"2023-09-26T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"date_updated":"2025-04-23T13:09:05Z","isi":1,"oa":1,"file_date_updated":"2024-01-30T14:33:31Z","_id":"14401","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":"        18","type":"journal_article","acknowledgement":"The authors would like to thank Mr. Joel Dietz for management of the mouse colony and helpful advice for conducting quantitative PCR studies and Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606 (RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences (University of Wisconsin-Madison) and to the Department of Ophthalmology (University of Rochester).","has_accepted_license":"1","ddc":["570"],"quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_MolecularNeurodegeneration_Maes.pdf","date_created":"2024-01-30T14:33:31Z","success":1,"creator":"dernst","file_id":"14917","file_size":11568350,"date_updated":"2024-01-30T14:33:31Z","access_level":"open_access","checksum":"3aa218ddea4a082d8fd5e196ae55ca06","relation":"main_file"}],"publication_identifier":{"eissn":["1750-1326"]},"doi":"10.1186/s13024-023-00659-8","publication":"Molecular Neurodegeneration","year":"2023","date_created":"2023-10-08T22:01:15Z","article_number":"67","title":"BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy."}],"external_id":{"pmid":["37752598"],"isi":["001071403800001"]},"publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085"},{"first_name":"Ryan J.","last_name":"Donahue","full_name":"Donahue, Ryan J."},{"last_name":"Schlamp","first_name":"Cassandra L.","full_name":"Schlamp, Cassandra L."},{"full_name":"Marola, Olivia J.","first_name":"Olivia J.","last_name":"Marola"},{"first_name":"Richard T.","last_name":"Libby","full_name":"Libby, Richard T."},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"volume":18},{"issue":"6665","doi":"10.1126/science.adk3070","publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","year":"2023","date_created":"2023-10-08T22:01:16Z","corr_author":"1","quality_controlled":"1","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Daniel","last_name":"Balazs","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"volume":381,"title":"Widening the use of 3D printing","page":"1413-1414","article_processing_charge":"No","abstract":[{"text":"A light-triggered fabrication method extends the functionality of printable nanomaterials","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001100656800023"],"pmid":["37769110"]},"day":"29","status":"public","citation":{"short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” <i>Science</i>, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. <i>Science</i>. 2023;381(6665):1413-1414. doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>.","apa":"Balazs, D., &#38; Ibáñez, M. (2023). Widening the use of 3D printing. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>."},"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"_id":"14404","scopus_import":"1","article_type":"letter_note","intvolume":"       381","oa_version":"None","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","type":"journal_article","language":[{"iso":"eng"}],"month":"09","date_published":"2023-09-29T00:00:00Z","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publisher":"AAAS","date_updated":"2025-09-09T13:04:47Z","isi":1},{"conference":{"start_date":"2023-09-19","name":"CONCUR: Conference on Concurrency Theory","location":"Antwerp, Belgium","end_date":"2023-09-22"},"ddc":["000"],"has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"14413","file_size":795790,"date_updated":"2023-10-09T07:42:45Z","access_level":"open_access","relation":"main_file","checksum":"215765e40454d806174ac0a223e8d6fa","file_name":"2023_LIPcs_Bartocci.pdf","content_type":"application/pdf","date_created":"2023-10-09T07:42:45Z","success":1,"creator":"dernst"}],"corr_author":"1","publication":"34th International Conference on Concurrency Theory","doi":"10.4230/LIPIcs.CONCUR.2023.21","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772990"]},"article_number":"21","date_created":"2023-10-08T22:01:16Z","year":"2023","title":"Hypernode automata","external_id":{"arxiv":["2305.02836"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs."}],"article_processing_charge":"Yes","related_material":{"record":[{"status":"public","relation":"later_version","id":"20866"}]},"volume":279,"author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Oliveira da Costa, Ana","orcid":"0000-0002-8741-5799","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","last_name":"Oliveira da Costa","first_name":"Ana"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"citation":{"ista":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 21.","ama":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata. In: <i>34th International Conference on Concurrency Theory</i>. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">10.4230/LIPIcs.CONCUR.2023.21</a>","short":"E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode automata,” in <i>34th International Conference on Concurrency Theory</i>, Antwerp, Belgium, 2023, vol. 279.","mla":"Bartocci, Ezio, et al. “Hypernode Automata.” <i>34th International Conference on Concurrency Theory</i>, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">10.4230/LIPIcs.CONCUR.2023.21</a>.","chicago":"Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Hypernode Automata.” In <i>34th International Conference on Concurrency Theory</i>, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.21</a>.","apa":"Bartocci, E., Henzinger, T. A., Nickovic, D., &#38; Oliveira da Costa, A. (2023). Hypernode automata. In <i>34th International Conference on Concurrency Theory</i> (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.21</a>"},"status":"public","day":"01","alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_updated":"2026-01-05T12:27:40Z","department":[{"_id":"ToHe"}],"arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2023-09-01T00:00:00Z","language":[{"iso":"eng"}],"month":"09","file_date_updated":"2023-10-09T07:42:45Z","oa":1,"scopus_import":"1","_id":"14405","type":"conference","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF) SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the ERC Advanced Grant\r\nVAMOS 101020093.","oa_version":"Published Version","intvolume":"       279"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.09455"}],"quality_controlled":"1","issue":"10","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"doi":"10.1103/PhysRevB.108.104205","publication":"Physical Review B","year":"2023","date_created":"2023-10-08T22:01:17Z","article_number":"104205","title":"Generalized surface multifractality in two-dimensional disordered systems","article_processing_charge":"No","abstract":[{"text":"Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model (\r\nNL\r\nσ\r\nM\r\n) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the \r\nNL\r\nσ\r\nM\r\n for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization.","lang":"eng"}],"external_id":{"isi":["001186160100001"],"arxiv":["2306.09455"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"41e64307-6672-11ee-b9ad-cc7a0075a479","orcid":"0009-0003-7382-8036","full_name":"Babkin, Serafim","last_name":"Babkin","first_name":"Serafim"},{"full_name":"Karcher, Jonas F.","last_name":"Karcher","first_name":"Jonas F."},{"full_name":"Burmistrov, Igor S.","last_name":"Burmistrov","first_name":"Igor S."},{"first_name":"Alexander D.","last_name":"Mirlin","full_name":"Mirlin, Alexander D."}],"volume":108,"citation":{"chicago":"Babkin, Serafim, Jonas F. Karcher, Igor S. Burmistrov, and Alexander D. Mirlin. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.104205\">https://doi.org/10.1103/PhysRevB.108.104205</a>.","apa":"Babkin, S., Karcher, J. F., Burmistrov, I. S., &#38; Mirlin, A. D. (2023). Generalized surface multifractality in two-dimensional disordered systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.104205\">https://doi.org/10.1103/PhysRevB.108.104205</a>","mla":"Babkin, Serafim, et al. “Generalized Surface Multifractality in Two-Dimensional Disordered Systems.” <i>Physical Review B</i>, vol. 108, no. 10, 104205, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.104205\">10.1103/PhysRevB.108.104205</a>.","ieee":"S. Babkin, J. F. Karcher, I. S. Burmistrov, and A. D. Mirlin, “Generalized surface multifractality in two-dimensional disordered systems,” <i>Physical Review B</i>, vol. 108, no. 10. American Physical Society, 2023.","short":"S. Babkin, J.F. Karcher, I.S. Burmistrov, A.D. Mirlin, Physical Review B 108 (2023).","ista":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. 2023. Generalized surface multifractality in two-dimensional disordered systems. Physical Review B. 108(10), 104205.","ama":"Babkin S, Karcher JF, Burmistrov IS, Mirlin AD. Generalized surface multifractality in two-dimensional disordered systems. <i>Physical Review B</i>. 2023;108(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.104205\">10.1103/PhysRevB.108.104205</a>"},"status":"public","day":"01","language":[{"iso":"eng"}],"month":"09","date_published":"2023-09-01T00:00:00Z","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","arxiv":1,"date_updated":"2025-09-09T13:03:44Z","isi":1,"oa":1,"_id":"14406","scopus_import":"1","article_type":"original","intvolume":"       108","oa_version":"Preprint","acknowledgement":"We thank Ilya Gruzberg for many illuminating discussions. S.S.B., J.F.K., and A.D.M. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) via the Grant\r\nNo. MI 658/14-1. I.S.B. acknowledges support from Russian Science Foundation (Grant No. 22-42-04416).","type":"journal_article"},{"publication":"European Journal of Organic Chemistry","doi":"10.1002/ejoc.202300769","publication_identifier":{"eissn":["1099-0690"],"issn":["1434-193X"]},"issue":"42","article_number":"e202300769","date_created":"2023-10-08T22:01:18Z","year":"2023","ddc":["540"],"has_accepted_license":"1","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_EurJOrgChem_Baunis.pdf","date_created":"2024-01-30T14:04:44Z","success":1,"creator":"dernst","file_id":"14913","date_updated":"2024-01-30T14:04:44Z","file_size":3277622,"access_level":"open_access","relation":"main_file","checksum":"e8ad7865acd94672e476f273ccf3d542"}],"corr_author":"1","volume":26,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Baunis","first_name":"Haralds","full_name":"Baunis, Haralds","id":"2eea55ec-e8ec-11ed-86cb-d9c76787acfe"},{"last_name":"Pieber","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus"}],"title":"Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex","publication_status":"published","external_id":{"isi":["001072666500001"]},"abstract":[{"lang":"eng","text":"We present a photon- and metal-free approach for the radical fluorination of aliphatic oxalate-activated alcohols. The method relies on the spontaneous generation of the N-(chloromethyl)triethylenediamine radical dication, a potent single electron oxidant, from Selectfluor and 4-(dimethylamino)pyridine. The protocol is easily scalable and provides the desired fluorinated products within only a few minutes reaction time."}],"article_processing_charge":"Yes (via OA deal)","status":"public","day":"07","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"citation":{"apa":"Baunis, H., &#38; Pieber, B. (2023). Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. <i>European Journal of Organic Chemistry</i>. Wiley. <a href=\"https://doi.org/10.1002/ejoc.202300769\">https://doi.org/10.1002/ejoc.202300769</a>","chicago":"Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer Complex.” <i>European Journal of Organic Chemistry</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/ejoc.202300769\">https://doi.org/10.1002/ejoc.202300769</a>.","mla":"Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer Complex.” <i>European Journal of Organic Chemistry</i>, vol. 26, no. 42, e202300769, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/ejoc.202300769\">10.1002/ejoc.202300769</a>.","ieee":"H. Baunis and B. Pieber, “Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex,” <i>European Journal of Organic Chemistry</i>, vol. 26, no. 42. Wiley, 2023.","short":"H. Baunis, B. Pieber, European Journal of Organic Chemistry 26 (2023).","ista":"Baunis H, Pieber B. 2023. Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal of Organic Chemistry. 26(42), e202300769.","ama":"Baunis H, Pieber B. Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. <i>European Journal of Organic Chemistry</i>. 2023;26(42). doi:<a href=\"https://doi.org/10.1002/ejoc.202300769\">10.1002/ejoc.202300769</a>"},"scopus_import":"1","_id":"14409","acknowledgement":"We gratefully acknowledge the Max-Planck Society and the Institute of Science and Technology Austria (ISTA) for generous financial support. We also thank the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2008 – 390540038 – UniSysCat for funding. B.P. thanks the Boehringer Ingelheim Foundation for funding through the Plus 3 Perspectives Programme.","type":"journal_article","oa_version":"Published Version","intvolume":"        26","article_type":"original","date_updated":"2024-10-09T21:07:03Z","department":[{"_id":"BaPi"}],"publisher":"Wiley","date_published":"2023-11-07T00:00:00Z","language":[{"iso":"eng"}],"month":"11","file_date_updated":"2024-01-30T14:04:44Z","oa":1,"isi":1},{"scopus_import":"1","_id":"14410","volume":14068,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","intvolume":"     14068","author":[{"first_name":"Paulina","last_name":"Tomaszewska","full_name":"Tomaszewska, Paulina"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"date_updated":"2023-10-09T06:48:02Z","department":[{"_id":"ChLa"}],"publisher":"Springer Nature","date_published":"2023-08-20T00:00:00Z","language":[{"iso":"eng"}],"title":"On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift","month":"08","publication_status":"published","abstract":[{"text":"This paper focuses on the implementation details of the baseline methods and a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming data under class-prior shift. LIMES achieves superior performance over the baseline methods, especially concerning the minimum-across-day accuracy, which is important for the users of the system. In this work, the key measures to facilitate reproducibility and enhance the credibility of the results are described.","lang":"eng"}],"article_processing_charge":"No","page":"67-73","status":"public","publication":"International Workshop on Reproducible Research in Pattern Recognition","day":"20","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031407727"],"issn":["0302-9743"]},"doi":"10.1007/978-3-031-40773-4_6","alternative_title":["LNCS"],"date_created":"2023-10-08T22:01:18Z","year":"2023","conference":{"name":"RRPR: Reproducible Research in Pattern Recognition","start_date":"2022-08-21","location":"Montreal, Canada","end_date":"2022-08-21"},"quality_controlled":"1","citation":{"ista":"Tomaszewska P, Lampert C. 2023. On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. International Workshop on Reproducible Research in Pattern Recognition. RRPR: Reproducible Research in Pattern Recognition, LNCS, vol. 14068, 67–73.","ama":"Tomaszewska P, Lampert C. On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. In: <i>International Workshop on Reproducible Research in Pattern Recognition</i>. Vol 14068. Springer Nature; 2023:67-73. doi:<a href=\"https://doi.org/10.1007/978-3-031-40773-4_6\">10.1007/978-3-031-40773-4_6</a>","short":"P. Tomaszewska, C. Lampert, in:, International Workshop on Reproducible Research in Pattern Recognition, Springer Nature, 2023, pp. 67–73.","ieee":"P. Tomaszewska and C. Lampert, “On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift,” in <i>International Workshop on Reproducible Research in Pattern Recognition</i>, Montreal, Canada, 2023, vol. 14068, pp. 67–73.","mla":"Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.” <i>International Workshop on Reproducible Research in Pattern Recognition</i>, vol. 14068, Springer Nature, 2023, pp. 67–73, doi:<a href=\"https://doi.org/10.1007/978-3-031-40773-4_6\">10.1007/978-3-031-40773-4_6</a>.","chicago":"Tomaszewska, Paulina, and Christoph Lampert. “On the Implementation of Baselines and Lightweight Conditional Model Extrapolation (LIMES) under Class-Prior Shift.” In <i>International Workshop on Reproducible Research in Pattern Recognition</i>, 14068:67–73. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-40773-4_6\">https://doi.org/10.1007/978-3-031-40773-4_6</a>.","apa":"Tomaszewska, P., &#38; Lampert, C. (2023). On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift. In <i>International Workshop on Reproducible Research in Pattern Recognition</i> (Vol. 14068, pp. 67–73). Montreal, Canada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-40773-4_6\">https://doi.org/10.1007/978-3-031-40773-4_6</a>"}},{"scopus_import":"1","_id":"14411","acknowledgement":"This work was supported by the Czech Foundation grant No. GA22-10845S, Grant Agency of Masaryk University grant No. MUNI/G/1771/2020, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","type":"conference","oa_version":"Submitted Version","intvolume":"     14137","date_updated":"2025-09-09T14:25:46Z","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"date_published":"2023-09-09T00:00:00Z","language":[{"iso":"eng"}],"month":"09","file_date_updated":"2024-02-16T08:26:32Z","oa":1,"isi":1,"day":"09","status":"public","alternative_title":["LNBI"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"citation":{"ista":"Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. 2023. Phenotype control of partially specified boolean networks. 21st International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNBI, vol. 14137, 18–35.","ama":"Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. Phenotype control of partially specified boolean networks. In: <i>21st International Conference on Computational Methods in Systems Biology</i>. Vol 14137. Springer Nature; 2023:18-35. doi:<a href=\"https://doi.org/10.1007/978-3-031-42697-1_2\">10.1007/978-3-031-42697-1_2</a>","ieee":"N. Beneš, L. Brim, S. Pastva, D. Šafránek, and E. Šmijáková, “Phenotype control of partially specified boolean networks,” in <i>21st International Conference on Computational Methods in Systems Biology</i>, Luxembourg City, Luxembourg, 2023, vol. 14137, pp. 18–35.","short":"N. Beneš, L. Brim, S. Pastva, D. Šafránek, E. Šmijáková, in:, 21st International Conference on Computational Methods in Systems Biology, Springer Nature, 2023, pp. 18–35.","mla":"Beneš, Nikola, et al. “Phenotype Control of Partially Specified Boolean Networks.” <i>21st International Conference on Computational Methods in Systems Biology</i>, vol. 14137, Springer Nature, 2023, pp. 18–35, doi:<a href=\"https://doi.org/10.1007/978-3-031-42697-1_2\">10.1007/978-3-031-42697-1_2</a>.","chicago":"Beneš, Nikola, Luboš Brim, Samuel Pastva, David Šafránek, and Eva Šmijáková. “Phenotype Control of Partially Specified Boolean Networks.” In <i>21st International Conference on Computational Methods in Systems Biology</i>, 14137:18–35. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-42697-1_2\">https://doi.org/10.1007/978-3-031-42697-1_2</a>.","apa":"Beneš, N., Brim, L., Pastva, S., Šafránek, D., &#38; Šmijáková, E. (2023). Phenotype control of partially specified boolean networks. In <i>21st International Conference on Computational Methods in Systems Biology</i> (Vol. 14137, pp. 18–35). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-42697-1_2\">https://doi.org/10.1007/978-3-031-42697-1_2</a>"},"volume":14137,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Beneš, Nikola","first_name":"Nikola","last_name":"Beneš"},{"last_name":"Brim","first_name":"Luboš","full_name":"Brim, Luboš"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel","last_name":"Pastva","first_name":"Samuel"},{"last_name":"Šafránek","first_name":"David","full_name":"Šafránek, David"},{"first_name":"Eva","last_name":"Šmijáková","full_name":"Šmijáková, Eva"}],"title":"Phenotype control of partially specified boolean networks","external_id":{"isi":["001156280600002"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Partially specified Boolean networks (PSBNs) represent a promising framework for the qualitative modelling of biological systems in which the logic of interactions is not completely known. Phenotype control aims to stabilise the network in states exhibiting specific traits.\r\nIn this paper, we define the phenotype control problem in the context of asynchronous PSBNs and propose a novel semi-symbolic algorithm for solving this problem with permanent variable perturbations."}],"article_processing_charge":"No","page":"18-35","publication":"21st International Conference on Computational Methods in Systems Biology","doi":"10.1007/978-3-031-42697-1_2","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031426964"]},"date_created":"2023-10-08T22:01:18Z","year":"2023","conference":{"location":"Luxembourg City, Luxembourg","end_date":"2023-09-15","name":"CMSB: Computational Methods in Systems Biology","start_date":"2023-09-13"},"ddc":["000"],"has_accepted_license":"1","quality_controlled":"1","file":[{"date_created":"2024-02-16T08:26:32Z","content_type":"application/pdf","file_name":"cmsb2023.pdf","creator":"spastva","success":1,"file_id":"14997","checksum":"6f71bdaedb770b52380222fd9f4d7937","relation":"main_file","access_level":"open_access","date_updated":"2024-02-16T08:26:32Z","file_size":691582}]},{"_id":"14417","scopus_import":"1","intvolume":"       272","oa_version":"Published Version","acknowledgement":"This work was partly funded by the ERC CoG 863818 (ForM-SMArt), the DFG Grant\r\n389792660 as part of TRR 248 (Foundations of Perspicuous Software Systems), the Cluster of\r\nExcellence EXC 2050/1 (CeTI, project ID 390696704, as part of Germany’s Excellence Strategy), and the DFG projects BA-1679/11-1 and BA-1679/12-1.","type":"conference","language":[{"iso":"eng"}],"month":"08","date_published":"2023-08-21T00:00:00Z","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","arxiv":1,"date_updated":"2025-09-08T09:10:05Z","oa":1,"file_date_updated":"2023-10-09T09:19:11Z","alternative_title":["LIPIcs"],"status":"public","day":"21","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"short":"C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, in:, 48th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” in <i>48th International Symposium on Mathematical Foundations of Computer Science</i>, Bordeaux, France, 2023, vol. 272.","ista":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2023. Entropic risk for turn-based stochastic games. 48th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 272, 15.","ama":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. In: <i>48th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2023.15\">10.4230/LIPIcs.MFCS.2023.15</a>","apa":"Baier, C., Chatterjee, K., Meggendorfer, T., &#38; Piribauer, J. (2023). Entropic risk for turn-based stochastic games. In <i>48th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 272). Bordeaux, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2023.15\">https://doi.org/10.4230/LIPIcs.MFCS.2023.15</a>","chicago":"Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” In <i>48th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 272. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2023.15\">https://doi.org/10.4230/LIPIcs.MFCS.2023.15</a>.","mla":"Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” <i>48th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 272, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2023.15\">10.4230/LIPIcs.MFCS.2023.15</a>."},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"related_material":{"record":[{"id":"17474","relation":"later_version","status":"public"}]},"author":[{"first_name":"Christel","last_name":"Baier","full_name":"Baier, Christel"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer"},{"full_name":"Piribauer, Jakob","first_name":"Jakob","last_name":"Piribauer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":272,"title":"Entropic risk for turn-based stochastic games","article_processing_charge":"Yes","abstract":[{"text":"Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. In the most general case, the problem is decidable subject to Shanuel’s conjecture. If all inputs are rational, the resulting threshold problem can be solved using algebraic numbers, leading to decidability via a polynomial-time reduction to the existential theory of the reals. Further restrictions on the encoding of the input allow the solution of the threshold problem in NP∩coNP. Finally, an approximation algorithm for the optimal value of ERisk is provided.","lang":"eng"}],"external_id":{"arxiv":["2307.06611"]},"publication_status":"published","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772921"]},"doi":"10.4230/LIPIcs.MFCS.2023.15","publication":"48th International Symposium on Mathematical Foundations of Computer Science","year":"2023","date_created":"2023-10-09T09:21:05Z","article_number":"15","has_accepted_license":"1","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2023-08-28","location":"Bordeaux, France","end_date":"2023-09-01"},"ddc":["000"],"corr_author":"1","file":[{"file_size":826843,"date_updated":"2023-10-09T09:19:11Z","access_level":"open_access","relation":"main_file","checksum":"402281b17ed669bbf149d0fdf68ac201","file_id":"14418","success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2023_LIPIcsMFCS_Baier.pdf","date_created":"2023-10-09T09:19:11Z"}],"quality_controlled":"1"},{"file":[{"success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2023_PloSBiology_Unterweger.pdf","date_created":"2023-10-16T07:20:49Z","date_updated":"2023-10-16T07:20:49Z","file_size":6193110,"access_level":"open_access","relation":"main_file","checksum":"40a2b11b41d70a0e5939f8a52b66e389","file_id":"14431"}],"quality_controlled":"1","ddc":["570"],"has_accepted_license":"1","article_number":"e3002315","date_created":"2023-10-15T22:01:10Z","year":"2023","publication":"PLoS Biology","doi":"10.1371/journal.pbio.3002315","publication_identifier":{"eissn":["1545-7885"]},"issue":"10","publication_status":"published","abstract":[{"lang":"eng","text":"To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type–specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver."}],"article_processing_charge":"No","title":"Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics","volume":21,"author":[{"full_name":"Unterweger, Iris A.","last_name":"Unterweger","first_name":"Iris A."},{"last_name":"Klepstad","first_name":"Julie","full_name":"Klepstad, Julie"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lundegaard, Pia R.","first_name":"Pia R.","last_name":"Lundegaard"},{"full_name":"Trusina, Ala","first_name":"Ala","last_name":"Trusina"},{"full_name":"Ober, Elke A.","last_name":"Ober","first_name":"Elke A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/JulieKlepstad/LiverDevelopment","relation":"software"}]},"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"citation":{"apa":"Unterweger, I. A., Klepstad, J., Hannezo, E. B., Lundegaard, P. R., Trusina, A., &#38; Ober, E. A. (2023). Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002315\">https://doi.org/10.1371/journal.pbio.3002315</a>","chicago":"Unterweger, Iris A., Julie Klepstad, Edouard B Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” <i>PLoS Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pbio.3002315\">https://doi.org/10.1371/journal.pbio.3002315</a>.","mla":"Unterweger, Iris A., et al. “Lineage Tracing Identifies Heterogeneous Hepatoblast Contribution to Cell Lineages and Postembryonic Organ Growth Dynamics.” <i>PLoS Biology</i>, vol. 21, no. 10, e3002315, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002315\">10.1371/journal.pbio.3002315</a>.","ieee":"I. A. Unterweger, J. Klepstad, E. B. Hannezo, P. R. Lundegaard, A. Trusina, and E. A. Ober, “Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics,” <i>PLoS Biology</i>, vol. 21, no. 10. Public Library of Science, 2023.","short":"I.A. Unterweger, J. Klepstad, E.B. Hannezo, P.R. Lundegaard, A. Trusina, E.A. Ober, PLoS Biology 21 (2023).","ista":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. 2023. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biology. 21(10), e3002315.","ama":"Unterweger IA, Klepstad J, Hannezo EB, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. <i>PLoS Biology</i>. 2023;21(10). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002315\">10.1371/journal.pbio.3002315</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"04","status":"public","file_date_updated":"2023-10-16T07:20:49Z","oa":1,"date_updated":"2025-04-14T07:52:27Z","publisher":"Public Library of Science","department":[{"_id":"EdHa"}],"date_published":"2023-10-04T00:00:00Z","language":[{"iso":"eng"}],"month":"10","type":"journal_article","acknowledgement":"We thank the Ober group for discussion and comments on the manuscript. We are grateful to\r\nDr. F. Lemaigre for feedback on the manuscript and Dr. T. Piotrowski for invaluable support.\r\nWe thank the department of experimental medicine (AEM) in Copenhagen for expert fish\r\ncare. We gratefully acknowledge the DanStem Imaging Platform (University of Copenhagen)\r\nfor support and assistance in this work.\r\nThis work is supported by Novo Nordisk Foundation grant NNF17CC0027852 (EAO);\r\nNordisk Foundation grant NNF19OC0058327 (EAO); Novo Nordisk Foundation grant\r\nNNF17OC0031204 (PRL); https://novonordiskfonden.dk/en/; Danish National\r\nResearch Foundation grant DNRF116 (EAO and AT); https://dg.dk/en/; John and Birthe Meyer\r\nFoundation (PRL) and European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement No. 851288 (EH).","intvolume":"        21","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"14426"}]