[{"scopus_import":"1","day":"20","article_processing_charge":"No","article_type":"letter_note","publication":"Physical Review A","citation":{"mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304"},"date_published":"2023-06-20T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters."}],"issue":"6","title":"Finite-range bias in fitting three-body loss to the zero-range model","status":"public","intvolume":" 107","_id":"13233","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"06","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"oa":1,"external_id":{"isi":["001019748000005"],"arxiv":["2302.01022"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.01022"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.L061304","article_number":"L061304","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"publisher":"American Physical Society","year":"2023","acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:31:52Z","volume":107,"author":[{"last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","full_name":"Agafonova, Sofya"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}]},{"date_published":"2023-07-08T00:00:00Z","article_type":"original","citation":{"ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5."},"publication":"npj Climate and Atmospheric Science","has_accepted_license":"1","article_processing_charge":"Yes","day":"08","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2023_npjclimate_Goswami.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1750712,"creator":"dernst","relation":"main_file","file_id":"13326","date_updated":"2023-07-31T08:00:01Z","date_created":"2023-07-31T08:00:01Z","checksum":"e9967d436a83b8ffcc6f58782e1f7500","success":1}],"intvolume":" 6","ddc":["550"],"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13256","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41612-023-00411-5","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001024920300002"]},"publication_identifier":{"eissn":["2397-3722"]},"month":"07","volume":6,"date_created":"2023-07-23T22:01:10Z","date_updated":"2023-08-02T06:38:07Z","author":[{"full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","last_name":"Goswami"},{"full_name":"An, Soon Il","last_name":"An","first_name":"Soon Il"}],"department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","year":"2023","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-07-31T08:00:01Z","article_number":"82"},{"issue":"7","abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"type":"journal_article","file":[{"file_id":"13339","relation":"main_file","date_created":"2023-08-01T06:58:34Z","date_updated":"2023-08-01T06:58:34Z","success":1,"checksum":"70de3c4878de6efe00dc56de2df8812f","file_name":"2023_GBE_Barata.pdf","access_level":"open_access","creator":"dernst","file_size":2382587,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"13260","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 15","status":"public","ddc":["570"],"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","citation":{"chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113"},"publication":"Genome biology and evolution","article_type":"original","file_date_updated":"2023-08-01T06:58:34Z","article_number":"evad113","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"author":[{"id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata","first_name":"Carolina","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"first_name":"Rhonda R.","last_name":"Snook","full_name":"Snook, Rhonda R."},{"full_name":"Ritchie, Michael G.","last_name":"Ritchie","first_name":"Michael G."},{"full_name":"Kosiol, Carolin","last_name":"Kosiol","first_name":"Carolin"}],"volume":15,"date_created":"2023-07-23T22:01:11Z","date_updated":"2023-08-02T06:42:35Z","pmid":1,"acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","year":"2023","publisher":"Oxford Academic","department":[{"_id":"BeVi"}],"publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"month":"07","doi":"10.1093/gbe/evad113","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"isi":1,"quality_controlled":"1"},{"date_published":"2023-01-10T00:00:00Z","publication":"ACS Nano","citation":{"mla":"Lionello, Chiara, et al. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano, vol. 17, no. 1, American Chemical Society, 2023, pp. 275–87, doi:10.1021/acsnano.2c07558.","short":"C. Lionello, C. Perego, A. Gardin, R. Klajn, G.M. Pavan, ACS Nano 17 (2023) 275–287.","chicago":"Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni M. Pavan. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.2c07558.","ama":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 2023;17(1):275-287. doi:10.1021/acsnano.2c07558","ista":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. 2023. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 17(1), 275–287.","ieee":"C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. M. Pavan, “Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices,” ACS Nano, vol. 17, no. 1. American Chemical Society, pp. 275–287, 2023.","apa":"Lionello, C., Perego, C., Gardin, A., Klajn, R., & Pavan, G. M. (2023). Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.2c07558"},"article_type":"original","page":"275-287","day":"10","article_processing_charge":"No","scopus_import":"1","keyword":["General Physics and Astronomy","General Engineering","General Materials Science"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13346","title":"Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices","status":"public","intvolume":" 17","abstract":[{"lang":"eng","text":"The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities."}],"issue":"1","type":"journal_article","doi":"10.1021/acsnano.2c07558","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1021/acsnano.2c07558","open_access":"1"}],"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"author":[{"last_name":"Lionello","first_name":"Chiara","full_name":"Lionello, Chiara"},{"first_name":"Claudio","last_name":"Perego","full_name":"Perego, Claudio"},{"first_name":"Andrea","last_name":"Gardin","full_name":"Gardin, Andrea"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"},{"full_name":"Pavan, Giovanni M.","first_name":"Giovanni M.","last_name":"Pavan"}],"date_updated":"2023-08-02T06:51:15Z","date_created":"2023-08-01T09:30:29Z","volume":17,"year":"2023","publication_status":"published","publisher":"American Chemical Society","extern":"1"},{"author":[{"first_name":"Daniel","last_name":"Huber","full_name":"Huber, Daniel"},{"full_name":"Pinsonneault, Marc","first_name":"Marc","last_name":"Pinsonneault"},{"first_name":"Paul","last_name":"Beck","full_name":"Beck, Paul"},{"full_name":"Bedding, Timothy R.","last_name":"Bedding","first_name":"Timothy R."},{"first_name":"Joss Bland-Hawthorn","last_name":"Joss Bland-Hawthorn","full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn"},{"first_name":"Sylvain N.","last_name":"Breton","full_name":"Breton, Sylvain N."},{"last_name":"Bugnet","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"Chaplin, William J.","first_name":"William J.","last_name":"Chaplin"},{"last_name":"Garcia","first_name":"Rafael A.","full_name":"Garcia, Rafael A."},{"first_name":"Samuel K.","last_name":"Grunblatt","full_name":"Grunblatt, Samuel K."},{"full_name":"Guzik, Joyce A.","last_name":"Guzik","first_name":"Joyce A."},{"full_name":"Hekker, Saskia","first_name":"Saskia","last_name":"Hekker"},{"first_name":"Steven D.","last_name":"Kawaler","full_name":"Kawaler, Steven D."},{"last_name":"Mathis","first_name":"Stephane","full_name":"Mathis, Stephane"},{"last_name":"Mathur","first_name":"Savita","full_name":"Mathur, Savita"},{"full_name":"Metcalfe, Travis","first_name":"Travis","last_name":"Metcalfe"},{"full_name":"Mosser, Benoit","last_name":"Mosser","first_name":"Benoit"},{"first_name":"Melissa K.","last_name":"Ness","full_name":"Ness, Melissa K."},{"full_name":"Piro, Anthony L.","last_name":"Piro","first_name":"Anthony L."},{"full_name":"Serenelli, Aldo","last_name":"Serenelli","first_name":"Aldo"},{"first_name":"Sanjib","last_name":"Sharma","full_name":"Sharma, Sanjib"},{"full_name":"Soderblom, David R.","last_name":"Soderblom","first_name":"David R."},{"full_name":"Stassun, Keivan G.","first_name":"Keivan G.","last_name":"Stassun"},{"first_name":"Dennis","last_name":"Stello","full_name":"Stello, Dennis"},{"full_name":"Tayar, Jamie","first_name":"Jamie","last_name":"Tayar"},{"full_name":"Belle, Gerard T. van","last_name":"Belle","first_name":"Gerard T. van"},{"full_name":"Zinn, Joel C.","last_name":"Zinn","first_name":"Joel C."}],"date_created":"2023-08-02T07:30:43Z","date_updated":"2023-08-02T07:36:00Z","oa_version":"Preprint","_id":"13447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publication_status":"submitted","title":"Asteroseismology with the Roman galactic bulge time-domain survey","status":"public","department":[{"_id":"LiBu"}],"abstract":[{"lang":"eng","text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing."}],"article_number":"2307.03237","type":"preprint","date_published":"2023-07-06T00:00:00Z","doi":"10.48550/arXiv.2307.03237","language":[{"iso":"eng"}],"publication":"arXiv","oa":1,"citation":{"chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.","short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.","ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.03237"}],"external_id":{"arxiv":["2307.03237"]},"month":"07","day":"06","article_processing_charge":"No"},{"doi":"10.1021/jacs.2c11973","language":[{"iso":"eng"}],"external_id":{"pmid":["36757850"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c11973"}],"oa":1,"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"author":[{"last_name":"Wang","first_name":"Jinhua","full_name":"Wang, Jinhua"},{"first_name":"Tzuf Shay","last_name":"Peled","full_name":"Peled, Tzuf Shay"},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"date_created":"2023-08-01T09:33:08Z","date_updated":"2023-08-02T10:44:22Z","volume":145,"year":"2023","pmid":1,"publication_status":"published","publisher":"American Chemical Society","extern":"1","date_published":"2023-02-09T00:00:00Z","publication":"Journal of the American Chemical Society","citation":{"short":"J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145 (2023) 4098–4108.","mla":"Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society, vol. 145, no. 7, American Chemical Society, 2023, pp. 4098–108, doi:10.1021/jacs.2c11973.","chicago":"Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.2c11973.","ama":"Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 2023;145(7):4098-4108. doi:10.1021/jacs.2c11973","ieee":"J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive nanoparticle aggregates,” Journal of the American Chemical Society, vol. 145, no. 7. American Chemical Society, pp. 4098–4108, 2023.","apa":"Wang, J., Peled, T. S., & Klajn, R. (2023). Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.2c11973","ista":"Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108."},"article_type":"original","page":"4098-4108","day":"09","article_processing_charge":"No","scopus_import":"1","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"oa_version":"Published Version","_id":"13354","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Photocleavable anionic glues for light-responsive nanoparticle aggregates","intvolume":" 145","abstract":[{"text":"Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.","lang":"eng"}],"issue":"7","type":"journal_article"},{"project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12781","month":"03","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"year":"2023","date_updated":"2023-08-04T08:54:51Z","date_created":"2023-03-31T12:24:42Z","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12138"}]},"file_date_updated":"2023-04-20T07:02:59Z","ec_funded":1,"page":"127","citation":{"chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781"},"date_published":"2023-03-23T00:00:00Z","day":"23","has_accepted_license":"1","article_processing_charge":"No","ddc":["570","572"],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","status":"public","_id":"12781","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_id":"12852","embargo":"2024-04-20","relation":"main_file","checksum":"5ebb6345cb4119f93460c81310265a6d","date_created":"2023-04-19T14:33:41Z","date_updated":"2023-04-19T14:33:41Z","access_level":"closed","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo_to":"local","creator":"vkravchu","file_size":6071553,"content_type":"application/pdf"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19468766,"creator":"vkravchu","access_level":"closed","embargo_to":"local","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","checksum":"c12055c48411d030d2afa51de2166221","date_updated":"2023-04-20T07:02:59Z","date_created":"2023-04-19T14:33:52Z","relation":"source_file","embargo":"2024-04-20","file_id":"12853"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}]},{"publication_identifier":{"issn":["2663-337X"]},"month":"05","doi":"10.15479/at:ista:13074","language":[{"iso":"eng"}],"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"file_date_updated":"2023-05-24T16:12:59Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11458"},{"id":"13053","status":"public","relation":"part_of_dissertation"},{"id":"12299","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"}],"date_created":"2023-05-23T17:07:53Z","date_updated":"2023-08-04T10:33:27Z","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"23","date_published":"2023-05-23T00:00:00Z","citation":{"ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074."},"page":"147","abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"creator":"epeste","file_size":2152072,"content_type":"application/pdf","access_level":"open_access","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","success":1,"checksum":"6b3354968403cb9d48cc5a83611fb571","date_updated":"2023-05-24T16:11:16Z","date_created":"2023-05-24T16:11:16Z","file_id":"13087","relation":"main_file"},{"creator":"epeste","file_size":1658293,"content_type":"application/zip","file_name":"PhD_Thesis_APeste.zip","access_level":"closed","date_updated":"2023-05-24T16:12:59Z","date_created":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_id":"13088","relation":"source_file"}],"oa_version":"Published Version","_id":"13074","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Efficiency and generalization of sparse neural networks","status":"public","ddc":["000"]},{"date_published":"2023-05-17T00:00:00Z","citation":{"ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964."},"page":"146","has_accepted_license":"1","article_processing_charge":"No","day":"17","file":[{"file_name":"thesis_boocock.pdf","embargo_to":"open_access","access_level":"closed","creator":"dboocock","file_size":40414730,"content_type":"application/pdf","file_id":"12988","embargo":"2024-05-17","relation":"main_file","date_created":"2023-05-17T13:39:54Z","date_updated":"2023-05-19T07:04:25Z","checksum":"d51240675fc6dc0e3f5dc0c902695d3a"},{"date_updated":"2023-05-17T14:35:13Z","date_created":"2023-05-17T13:39:53Z","checksum":"581a2313ffeb40fe77e8a122a25a7795","relation":"source_file","file_id":"12989","file_size":34338567,"content_type":"application/zip","creator":"dboocock","file_name":"thesis_boocock.zip","access_level":"closed"}],"oa_version":"Published Version","_id":"12964","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["530"],"title":"Mechanochemical pattern formation across biological scales","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:12964","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"}],"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"month":"05","related_material":{"record":[{"id":"8602","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-15T14:52:36Z","date_updated":"2023-08-04T11:02:40Z","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-05-19T07:04:25Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"article_number":"054201","ec_funded":1,"file_date_updated":"2023-08-07T09:48:08Z","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60].","year":"2023","volume":108,"date_created":"2023-08-05T18:25:22Z","date_updated":"2023-08-07T09:51:39Z","author":[{"full_name":"Brighi, Pietro","first_name":"Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729"},{"full_name":"Ljubotina, Marko","last_name":"Ljubotina","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"08","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2303.16876"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.108.054201","type":"journal_article","issue":"5","abstract":[{"text":"The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons.","lang":"eng"}],"intvolume":" 108","status":"public","ddc":["530"],"title":"Many-body localization proximity effect in a two-species bosonic Hubbard model","_id":"13963","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"13981","checksum":"f763000339b5fd543c14377109920690","success":1,"date_created":"2023-08-07T09:48:08Z","date_updated":"2023-08-07T09:48:08Z","access_level":"open_access","file_name":"2023_PhysRevB_Brighi.pdf","file_size":3051398,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","article_type":"original","citation":{"ama":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201","ista":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201.","apa":"Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201","ieee":"P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023.","mla":"Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201.","short":"P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).","chicago":"Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201."},"publication":"Physical Review B","date_published":"2023-08-01T00:00:00Z"},{"issue":"4","abstract":[{"lang":"eng","text":"We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams."}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13966","intvolume":" 108","status":"public","title":"Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2023-07-15T00:00:00Z","citation":{"ama":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115","ieee":"G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023.","apa":"Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115","ista":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115.","short":"G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.","chicago":"Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115."},"publication":"Physical Review B","article_type":"original","ec_funded":1,"article_number":"045115","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo"},{"full_name":"Ho, Quoc P","first_name":"Quoc P","last_name":"Ho","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"Tscherbul, T. V.","first_name":"T. V.","last_name":"Tscherbul"}],"volume":108,"date_created":"2023-08-06T22:01:10Z","date_updated":"2023-08-07T08:41:29Z","year":"2023","acknowledgement":"We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC.","publisher":"American Physical Society","department":[{"_id":"MiLe"},{"_id":"TaHa"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"07","doi":"10.1103/PhysRevB.108.045115","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2203.12666"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12666","open_access":"1"}],"project":[{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751"},{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.15227/orgsyn.100.0271","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.15227/orgsyn.100.0271","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["2333-3553"],"issn":["0078-6209"]},"month":"07","volume":100,"date_updated":"2023-08-07T08:21:45Z","date_created":"2023-08-06T22:01:11Z","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"full_name":"Sletten, Eric T.","last_name":"Sletten","first_name":"Eric T."},{"first_name":"Cristian","last_name":"Cavedon","full_name":"Cavedon, Cristian"},{"full_name":"Seeberger, Peter H.","first_name":"Peter H.","last_name":"Seeberger"},{"full_name":"Pieber, Bartholomäus","last_name":"Pieber","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"}],"publisher":"Organic Syntheses","department":[{"_id":"BaPi"}],"publication_status":"published","year":"2023","date_published":"2023-07-01T00:00:00Z","page":"271-286","article_type":"original","citation":{"mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.","short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271","ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271","ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. 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We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","year":"2023","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"12945"}]},"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","last_name":"Bod'Ová","full_name":"Bod'Ová, Katarína"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"volume":14,"date_created":"2023-06-11T22:00:40Z","date_updated":"2023-08-07T13:09:09Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"03","citation":{"apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y."},"publication":"Nature Communications","article_type":"original","date_published":"2023-06-03T00:00:00Z","type":"journal_article","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13127","intvolume":" 14","status":"public","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"4af0393e3ed47b3fc46e68b81c3c1007","success":1,"date_created":"2023-06-13T08:05:46Z","date_updated":"2023-06-13T08:05:46Z","relation":"main_file","file_id":"13132","content_type":"application/pdf","file_size":2358167,"creator":"dernst","access_level":"open_access","file_name":"2023_NatureComm_CasillasPerez.pdf"}]},{"day":"12","has_accepted_license":"1","article_processing_charge":"No","keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"date_published":"2023-05-12T00:00:00Z","citation":{"ama":"Cremer S. 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This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-04-28T00:00:00Z","citation":{"ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885."},"page":"82","day":"28","article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","first_name":"Mariano"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10806"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"status":"public","relation":"part_of_dissertation","id":"12237"},{"id":"9118","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10123"}]},"date_created":"2023-05-02T07:58:57Z","date_updated":"2023-08-14T07:25:26Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"file_date_updated":"2023-05-02T07:43:18Z","ec_funded":1,"doi":"10.15479/at:ista:12885","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]}},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","publication":"Annales Henri Poincare","citation":{"ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","apa":"Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750."},"article_type":"original","page":"717-750","abstract":[{"lang":"eng","text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"14051","checksum":"8c7b185eba5ccd92ef55c120f654222c","success":1,"date_created":"2023-08-14T11:38:28Z","date_updated":"2023-08-14T11:38:28Z","access_level":"open_access","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","file_size":554871,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12087","ddc":["510"],"status":"public","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","intvolume":" 24","month":"03","publication_identifier":{"issn":["1424-0637"]},"doi":"10.1007/s00023-022-01220-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2105.08303"],"isi":["000837499800002"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"file_date_updated":"2023-08-14T11:38:28Z","ec_funded":1,"author":[{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth"},{"full_name":"Zhang, Haonan","first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"date_updated":"2023-08-14T11:39:28Z","date_created":"2022-09-11T22:01:57Z","volume":24,"year":"2023","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}]},{"date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"501-554","publication":"Israel Journal of Mathematics","citation":{"ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"scopus_import":"1","file":[{"creator":"vkaluza","file_size":900422,"content_type":"application/pdf","access_level":"open_access","file_name":"separated_nets.pdf","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","date_created":"2021-07-14T07:41:50Z","date_updated":"2021-07-14T07:41:50Z","file_id":"9653","relation":"main_file"}],"oa_version":"Submitted Version","title":"Highly irregular separated nets","ddc":["515","516"],"status":"public","intvolume":" 253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9652","abstract":[{"text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s11856-022-2448-6","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1903.05923"],"isi":["000904950300003"]},"oa":1,"month":"03","publication_identifier":{"eissn":["1565-8511"]},"date_updated":"2023-08-14T11:26:34Z","date_created":"2021-07-14T07:01:28Z","volume":253,"author":[{"last_name":"Dymond","first_name":"Michael","full_name":"Dymond, Michael"},{"last_name":"Kaluza","first_name":"Vojtech","orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","full_name":"Kaluza, Vojtech"}],"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","file_date_updated":"2021-07-14T07:41:50Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices."}],"intvolume":" 613","status":"public","title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12113","oa_version":"None","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","article_processing_charge":"No","day":"15","article_type":"original","citation":{"ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101","ieee":"L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023.","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.","chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101."},"publication":"Applied Surface Science","date_published":"2023-03-15T00:00:00Z","article_number":"156101","publisher":"Elsevier","department":[{"_id":"MaIb"}],"publication_status":"epub_ahead","acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","year":"2023","volume":613,"date_created":"2023-01-12T11:55:02Z","date_updated":"2023-08-14T11:47:06Z","author":[{"last_name":"Zhang","first_name":"Li","full_name":"Zhang, Li"},{"full_name":"Liu, Xingyu","first_name":"Xingyu","last_name":"Liu"},{"full_name":"Wu, Ting","first_name":"Ting","last_name":"Wu"},{"full_name":"Xu, Shengduo","last_name":"Xu","first_name":"Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f"},{"first_name":"Guoquan","last_name":"Suo","full_name":"Suo, Guoquan"},{"first_name":"Xiaohui","last_name":"Ye","full_name":"Ye, Xiaohui"},{"last_name":"Hou","first_name":"Xiaojiang","full_name":"Hou, Xiaojiang"},{"first_name":"Yanling","last_name":"Yang","full_name":"Yang, Yanling"},{"first_name":"Qingfeng","last_name":"Liu","full_name":"Liu, Qingfeng"},{"last_name":"Wang","first_name":"Hongqiang","full_name":"Wang, Hongqiang"}],"publication_identifier":{"issn":["0169-4332"]},"month":"03","isi":1,"quality_controlled":"1","external_id":{"isi":["000911497000001"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.apsusc.2022.156101"},{"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2102.07452"],"isi":["000799715600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s40072-022-00254-w","publication_identifier":{"issn":["2194-0401"]},"month":"09","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"publication_status":"published","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2023","volume":11,"date_updated":"2023-08-14T11:51:47Z","date_created":"2021-10-23T10:50:22Z","author":[{"full_name":"Clozeau, Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas","last_name":"Clozeau"}],"file_date_updated":"2023-08-14T11:51:04Z","page":"1254–1378","article_type":"original","citation":{"short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w","ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.","ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378."},"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","date_published":"2023-09-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","intvolume":" 11","ddc":["510"],"status":"public","title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10173","oa_version":"Published Version","file":[{"file_id":"14052","relation":"main_file","success":1,"checksum":"f83dcaecdbd3ace862c4ed97a20e8501","date_updated":"2023-08-14T11:51:04Z","date_created":"2023-08-14T11:51:04Z","access_level":"open_access","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","creator":"dernst","content_type":"application/pdf","file_size":1635193}],"type":"journal_article","abstract":[{"lang":"eng","text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods."}]},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":782278,"creator":"dernst","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","access_level":"open_access","date_updated":"2023-08-14T12:47:32Z","date_created":"2023-08-14T12:47:32Z","checksum":"b9247827dae5544d1d19c37abe547abc","success":1,"relation":"main_file","file_id":"14054"}],"_id":"11741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quenched universality for deformed Wigner matrices","ddc":["510"],"status":"public","intvolume":" 185","abstract":[{"text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.","lang":"eng"}],"type":"journal_article","date_published":"2023-04-01T00:00:00Z","publication":"Probability Theory and Related Fields","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7."},"article_type":"original","page":"1183–1218","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J"}],"date_updated":"2023-08-14T12:48:09Z","date_created":"2022-08-07T22:02:00Z","volume":185,"acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2023","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","file_date_updated":"2023-08-14T12:47:32Z","doi":"10.1007/s00440-022-01156-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2106.10200"],"isi":["000830344500001"]},"isi":1,"quality_controlled":"1","month":"04","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12331","intvolume":" 35","ddc":["540"],"title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","status":"public","oa_version":"Published Version","file":[{"file_id":"14055","relation":"main_file","success":1,"checksum":"b21dca2aa7a80c068bc256bdd1fea9df","date_updated":"2023-08-14T12:57:25Z","date_created":"2023-08-14T12:57:25Z","access_level":"open_access","file_name":"2023_ChemistryMaterials_Wang.pdf","creator":"dernst","file_size":2961043,"content_type":"application/pdf"}],"type":"journal_article","issue":"2","abstract":[{"text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance.","lang":"eng"}],"citation":{"chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542"},"publication":"Chemistry of Materials","page":"755-763","article_type":"original","date_published":"2023-01-24T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"24","acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","year":"2023","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","publication_status":"published","author":[{"first_name":"Siqi","last_name":"Wang","full_name":"Wang, Siqi"},{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","first_name":"Cheng"},{"first_name":"Shulin","last_name":"Bai","full_name":"Bai, Shulin"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"first_name":"Yingcai","last_name":"Zhu","full_name":"Zhu, Yingcai"},{"last_name":"Zhan","first_name":"Shaoping","full_name":"Zhan, Shaoping"},{"full_name":"Zheng, Junqing","last_name":"Zheng","first_name":"Junqing"},{"first_name":"Shuwei","last_name":"Tang","full_name":"Tang, Shuwei"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"volume":35,"date_updated":"2023-08-14T12:57:44Z","date_created":"2023-01-22T23:00:55Z","file_date_updated":"2023-08-14T12:57:25Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000914749700001"]},"oa":1,"project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"isi":1,"quality_controlled":"1","doi":"10.1021/acs.chemmater.2c03542","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"month":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11999","intvolume":" 69","ddc":["510"],"status":"public","title":"Inserting one edge into a simple drawing is hard","file":[{"relation":"main_file","file_id":"12006","date_updated":"2022-08-29T11:23:15Z","date_created":"2022-08-29T11:23:15Z","checksum":"def7ae3b28d9fd6aec16450e40090302","success":1,"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","file_size":1002218,"content_type":"application/pdf","creator":"alisjak"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles."}],"citation":{"mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023."},"publication":"Discrete and Computational Geometry","page":"745–770","article_type":"original","date_published":"2023-04-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","year":"2023","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M"},{"first_name":"Fabian","last_name":"Klute","full_name":"Klute, Fabian"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"last_name":"Vogtenhuber","first_name":"Birgit","full_name":"Vogtenhuber, Birgit"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"first_name":"Tilo","last_name":"Wiedera","full_name":"Wiedera, Tilo"}],"volume":69,"date_created":"2022-08-28T22:02:01Z","date_updated":"2023-08-14T12:51:25Z","ec_funded":1,"file_date_updated":"2022-08-29T11:23:15Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00454-022-00394-9","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"04"},{"author":[{"full_name":"Aksenov, Vitalii","last_name":"Aksenov","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Alexandra","last_name":"Drozdova","full_name":"Drozdova, Alexandra"},{"full_name":"Mohtashami, Amirkeivan","first_name":"Amirkeivan","last_name":"Mohtashami"}],"date_updated":"2023-08-14T12:54:32Z","date_created":"2023-01-22T23:00:55Z","volume":36,"year":"2023","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Springer Nature","month":"09","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"doi":"10.1007/s00446-022-00441-x","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2008.01009"],"isi":["000913424000001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01009"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12330","title":"The splay-list: A distribution-adaptive concurrent skip-list","status":"public","intvolume":" 36","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-09-01T00:00:00Z","publication":"Distributed Computing","citation":{"chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x"},"article_type":"original","page":"395-418"},{"file_date_updated":"2023-08-16T08:15:41Z","year":"2023","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"date_created":"2023-01-12T12:09:17Z","date_updated":"2023-08-16T08:18:47Z","volume":32,"month":"03","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"doi":"10.1111/mec.16793","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"issue":"6","_id":"12159","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"On the origin and structure of haplotype blocks","intvolume":" 32","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14062","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","success":1,"file_name":"2023_MolecularEcology_Shipilina.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7144607,"creator":"dernst"}],"scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Molecular Ecology","citation":{"ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457."},"article_type":"original","page":"1441-1457","date_published":"2023-03-01T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Structural Biology"],"date_published":"2023-01-01T00:00:00Z","citation":{"ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023)."},"publication":"Journal of Structural Biology: X","article_type":"original","abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"type":"journal_article","file":[{"file_size":5132322,"content_type":"application/pdf","creator":"dernst","file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access","date_created":"2023-08-16T09:36:28Z","date_updated":"2023-08-16T09:36:28Z","checksum":"b4b1c10a31018aafe053b7d55a470e54","success":1,"relation":"main_file","file_id":"14064"}],"oa_version":"Published Version","_id":"12114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","status":"public","ddc":["570"],"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","publication_identifier":{"issn":["2590-1524"]},"month":"01","doi":"10.1016/j.yjsbx.2022.100079","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["36578472"]},"quality_controlled":"1","file_date_updated":"2023-08-16T09:36:28Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_number":"100079","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"full_name":"Lebedenko, Olga O.","first_name":"Olga O.","last_name":"Lebedenko"},{"orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie","full_name":"Becker, Lea Marie"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"}],"volume":7,"date_created":"2023-01-12T11:55:38Z","date_updated":"2023-08-16T09:37:25Z","pmid":1,"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","year":"2023","department":[{"_id":"PaSc"}],"publisher":"Elsevier","publication_status":"published"},{"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"review","page":"762-777","publication":"FEBS Letters","citation":{"ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540."},"date_published":"2023-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"issue":"6","status":"public","title":"In vitro reconstitution of small GTPase regulation","ddc":["570"],"intvolume":" 597","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12163","oa_version":"Published Version","file":[{"file_id":"14063","relation":"main_file","success":1,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","date_created":"2023-08-16T08:31:04Z","date_updated":"2023-08-16T08:31:04Z","access_level":"open_access","file_name":"2023_FEBSLetters_Loose.pdf","creator":"dernst","file_size":3148143,"content_type":"application/pdf"}],"month":"03","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/1873-3468.14540","file_date_updated":"2023-08-16T08:31:04Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"MaLo"}],"year":"2023","acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","pmid":1,"date_updated":"2023-08-16T08:32:29Z","date_created":"2023-01-12T12:09:58Z","volume":597,"author":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"orcid":"0000-0002-3580-2906","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","last_name":"Auer","first_name":"Albert","full_name":"Auer, Albert"},{"id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","last_name":"Brognara","full_name":"Brognara, Gabriel"},{"last_name":"Budiman","first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R"},{"first_name":"Lukasz M","last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M"},{"full_name":"Matijevic, Ivana","first_name":"Ivana","last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd"}]},{"publication":"Distributed Computing","citation":{"short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43."},"article_type":"original","page":"29-43","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12164","status":"public","title":"Long-lived counters with polylogarithmic amortized step complexity","intvolume":" 36","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"external_id":{"isi":["000890138700001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00446-022-00439-5","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","year":"2023","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","author":[{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad"},{"full_name":"Hendler, Danny","first_name":"Danny","last_name":"Hendler"},{"last_name":"Milani","first_name":"Alessia","full_name":"Milani, Alessia"},{"full_name":"Travers, Corentin","first_name":"Corentin","last_name":"Travers"}],"date_created":"2023-01-12T12:10:08Z","date_updated":"2023-08-16T08:39:36Z","volume":36},{"_id":"12172","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 78","title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","status":"public","oa_version":"None","type":"journal_article","issue":"Part 1","abstract":[{"text":"In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case.","lang":"eng"}],"citation":{"short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47.","mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.","chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037","apa":"Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.","ista":"Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47."},"publication":"Materials Today: Proceedings","page":"40-47","article_type":"original","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","keyword":["General Medicine"],"article_processing_charge":"No","day":"20","year":"2023","publisher":"Elsevier","department":[{"_id":"BjHo"}],"publication_status":"published","author":[{"full_name":"Khatoon, Bushra","last_name":"Khatoon","first_name":"Bushra"},{"full_name":"Kamil, Shoaib","last_name":"Kamil","first_name":"Shoaib","id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9"},{"last_name":"Babu","first_name":"Hitesh","full_name":"Babu, Hitesh"},{"first_name":"M.","last_name":"Siraj Alam","full_name":"Siraj Alam, M."}],"volume":78,"date_updated":"2023-08-16T09:08:11Z","date_created":"2023-01-12T12:11:26Z","quality_controlled":"1","doi":"10.1016/j.matpr.2022.11.037","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2214-7853"]},"month":"03"},{"type":"journal_article","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"ddc":["570"],"status":"public","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12515","oa_version":"Published Version","file":[{"checksum":"49cd40f3bda6f267079427042e7d15e3","success":1,"date_updated":"2023-02-06T07:56:14Z","date_created":"2023-02-06T07:56:14Z","relation":"main_file","file_id":"12518","content_type":"application/pdf","file_size":21943473,"creator":"dernst","access_level":"open_access","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf"}],"scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Frontiers in Neuroanatomy","citation":{"ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467."},"date_published":"2023-01-10T00:00:00Z","article_number":"1097467","file_date_updated":"2023-02-06T07:56:14Z","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Frontiers","year":"2023","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","pmid":1,"date_updated":"2023-08-16T11:37:52Z","date_created":"2023-02-05T23:01:00Z","volume":16,"author":[{"full_name":"Ortiz-Leal, Irene","first_name":"Irene","last_name":"Ortiz-Leal"},{"first_name":"Mateo V.","last_name":"Torres","full_name":"Torres, Mateo V."},{"full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","last_name":"Vargas Barroso"},{"full_name":"Fidalgo, Luis Eusebio","first_name":"Luis Eusebio","last_name":"Fidalgo"},{"full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro","first_name":"Ana María"},{"first_name":"Jorge A.","last_name":"Larriva-Sahd","full_name":"Larriva-Sahd, Jorge A."},{"full_name":"Sánchez-Quinteiro, Pablo","last_name":"Sánchez-Quinteiro","first_name":"Pablo"}],"month":"01","publication_identifier":{"eissn":["1662-5129"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"language":[{"iso":"eng"}],"doi":"10.3389/fnana.2022.1097467"},{"date_published":"2023-06-01T00:00:00Z","article_type":"original","page":"813–823","publication":"Nature Biotechnology","citation":{"ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_NatureBioTech_Yeung.pdf","creator":"dernst","file_size":12040976,"content_type":"application/pdf","file_id":"14066","relation":"main_file","success":1,"checksum":"668447a1c8d360b68f8aaf9e08ed644f","date_updated":"2023-08-16T11:30:45Z","date_created":"2023-08-16T11:30:45Z"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","ddc":["570"],"status":"public","intvolume":" 41","_id":"12106","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41587-022-01560-3","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000909067600003"]},"month":"06","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"date_updated":"2023-08-16T11:32:33Z","date_created":"2023-01-08T23:00:53Z","volume":41,"author":[{"orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung","first_name":"Jake","full_name":"Yeung, Jake"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"full_name":"Zeller, Peter","last_name":"Zeller","first_name":"Peter"},{"full_name":"De Barbanson, Buys Anton","first_name":"Buys Anton","last_name":"De Barbanson"},{"first_name":"Max D.","last_name":"Wellenstein","full_name":"Wellenstein, Max D."},{"last_name":"Van Oudenaarden","first_name":"Alexander","full_name":"Van Oudenaarden, Alexander"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ScienComp"}],"year":"2023","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","file_date_updated":"2023-08-16T11:30:45Z"},{"ec_funded":1,"author":[{"full_name":"Boccato, Chiara","last_name":"Boccato","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"volume":24,"date_created":"2023-01-15T23:00:52Z","date_updated":"2023-08-16T11:34:03Z","year":"2023","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"month":"05","doi":"10.1007/s00023-022-01252-3","language":[{"iso":"eng"}],"external_id":{"arxiv":["2205.15284"],"isi":["000910751800002"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.15284"}],"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit."}],"type":"journal_article","oa_version":"Preprint","_id":"12183","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","title":"The Bose Gas in a box with Neumann boundary conditions","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","citation":{"apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023.","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3."},"publication":"Annales Henri Poincare","page":"1505-1560","article_type":"original"},{"month":"02","publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"doi":"10.1021/acs.jcim.2c01346","language":[{"iso":"eng"}],"file_date_updated":"2023-08-16T12:21:13Z","ec_funded":1,"year":"2023","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","pmid":1,"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"American Chemical Society","author":[{"full_name":"Koehl, Patrice","last_name":"Koehl","first_name":"Patrice"},{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-16T12:22:07Z","volume":63,"scopus_import":"1","day":"13","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of Chemical Information and Modeling","citation":{"apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346."},"article_type":"original","page":"973-985","date_published":"2023-02-13T00:00:00Z","type":"journal_article","abstract":[{"text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software.","lang":"eng"}],"issue":"3","_id":"12544","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510","540"],"status":"public","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","intvolume":" 63","file":[{"relation":"main_file","file_id":"14070","checksum":"7d20562269edff1e31b9d6019d4983b0","success":1,"date_created":"2023-08-16T12:21:13Z","date_updated":"2023-08-16T12:21:13Z","access_level":"open_access","file_name":"2023_JCIM_Koehl.pdf","content_type":"application/pdf","file_size":8069223,"creator":"dernst"}],"oa_version":"Published Version"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"450-460","publication":"Nature Ecology and Evolution","citation":{"apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6."},"abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"8244f4650a0e7aeea488d1bcd4a31702","date_updated":"2023-08-16T11:54:59Z","date_created":"2023-08-16T11:54:59Z","file_id":"14069","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1600499,"access_level":"open_access","file_name":"2023_NatureEcoEvo_Stock.pdf"}],"status":"public","title":"Pathogen evasion of social immunity","ddc":["570"],"intvolume":" 7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12543","month":"03","publication_identifier":{"eissn":["2397-334X"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41559-023-01981-6","quality_controlled":"1","isi":1,"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"oa":1,"file_date_updated":"2023-08-16T11:54:59Z","ec_funded":1,"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-16T11:55:48Z","volume":7,"author":[{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Milutinovic, Barbara","last_name":"Milutinovic","first_name":"Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","last_name":"Hönigsberger","first_name":"Michaela"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"id":"39523C54-F248-11E8-B48F-1D18A9856A87","last_name":"Wiesenhofer","first_name":"Florian","full_name":"Wiesenhofer, Florian"},{"full_name":"Kampleitner, Niklas","last_name":"Kampleitner","first_name":"Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan"},{"last_name":"Schmitt","first_name":"Thomas","full_name":"Schmitt, Thomas"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","year":"2023","pmid":1},{"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-02-01T00:00:00Z","publication":"Evolution Letters","citation":{"ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004."},"article_type":"original","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"issue":"1","type":"journal_article","file":[{"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","success":1,"date_updated":"2023-08-16T11:43:33Z","date_created":"2023-08-16T11:43:33Z","relation":"main_file","file_id":"14068","content_type":"application/pdf","file_size":2592189,"creator":"dernst","access_level":"open_access","file_name":"2023_EvLetters_Mrnjavac.pdf"}],"oa_version":"Published Version","_id":"12521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","ddc":["570"],"status":"public","intvolume":" 7","month":"02","publication_identifier":{"issn":["2056-3744"]},"doi":"10.1093/evlett/qrac004","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"file_date_updated":"2023-08-16T11:43:33Z","ec_funded":1,"article_number":"qrac004","author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea"},{"full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"date_created":"2023-02-06T13:59:12Z","date_updated":"2023-08-16T11:44:32Z","volume":7,"year":"2023","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"BeVi"}]},{"file_date_updated":"2023-08-16T12:29:06Z","ec_funded":1,"article_number":"102695","author":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"date_created":"2023-02-26T12:24:21Z","date_updated":"2023-08-16T12:30:25Z","volume":79,"acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","month":"04","publication_identifier":{"issn":["0959-4388"]},"doi":"10.1016/j.conb.2023.102695","language":[{"iso":"eng"}],"external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"abstract":[{"lang":"eng","text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression."}],"issue":"4","type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","date_created":"2023-08-16T12:29:06Z","date_updated":"2023-08-16T12:29:06Z","file_id":"14071","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1787894,"access_level":"open_access","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf"}],"_id":"12679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","status":"public","intvolume":" 79","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["General Neuroscience"],"date_published":"2023-04-01T00:00:00Z","publication":"Current Opinion in Neurobiology","citation":{"mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.","ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023."},"article_type":"review"},{"publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"month":"04","doi":"10.1002/mana.202100192","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["2104.05063"],"isi":["000914134900001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2023-08-16T11:40:02Z","author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"},{"last_name":"Lindemulder","first_name":"Nick","full_name":"Lindemulder, Nick"},{"full_name":"Veraar, Mark","first_name":"Mark","last_name":"Veraar"}],"volume":296,"date_created":"2023-01-29T23:00:59Z","date_updated":"2023-08-16T11:41:42Z","year":"2023","acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","department":[{"_id":"JuFi"}],"publisher":"Wiley","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350. doi:10.1002/mana.202100192","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","apa":"Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202100192","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” Mathematische Nachrichten, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:10.1002/mana.202100192.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten. Wiley, 2023. https://doi.org/10.1002/mana.202100192."},"publication":"Mathematische Nachrichten","page":"1319-1350","article_type":"original","issue":"4","abstract":[{"text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":449280,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_MathNachrichten_Agresti.pdf","checksum":"6f099f1d064173784d1a27716a2cc795","success":1,"date_created":"2023-08-16T11:40:02Z","date_updated":"2023-08-16T11:40:02Z","relation":"main_file","file_id":"14067"}],"_id":"12429","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 296","title":"On the trace embedding and its applications to evolution equations","status":"public","ddc":["510"]},{"month":"01","publication_identifier":{"issn":["0129-055X"]},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2110.00458","open_access":"1"}],"external_id":{"isi":["000909760300001"],"arxiv":["2110.00458"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1142/S0129055X2350006X","language":[{"iso":"eng"}],"article_number":"2350006","year":"2023","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing","author":[{"first_name":"Marco","last_name":"Falconi","full_name":"Falconi, Marco"},{"full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","first_name":"Nikolai K","last_name":"Leopold"},{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P"}],"date_updated":"2023-08-16T11:47:27Z","date_created":"2023-01-29T23:00:59Z","volume":35,"scopus_import":"1","day":"09","article_processing_charge":"No","publication":"Reviews in Mathematical Physics","citation":{"chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/S0129055X2350006X.","mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” Reviews in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X","ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 2023;35(4). doi:10.1142/S0129055X2350006X"},"article_type":"original","date_published":"2023-01-09T00:00:00Z","type":"journal_article","abstract":[{"text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively.","lang":"eng"}],"issue":"4","_id":"12430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","status":"public","intvolume":" 35","oa_version":"Preprint"},{"abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"type":"journal_article","file":[{"checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","success":1,"date_created":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:39:57Z","relation":"main_file","file_id":"14073","file_size":4474284,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_NatureCompScience_Lombardi.pdf"}],"oa_version":"Published Version","_id":"12762","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","intvolume":" 3","day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-20T00:00:00Z","publication":"Nature Computational Science","citation":{"chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9"},"article_type":"original","page":"254-263","file_date_updated":"2023-08-16T12:39:57Z","ec_funded":1,"author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio"},{"full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver","last_name":"Pepic"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"date_updated":"2023-08-16T12:41:53Z","date_created":"2023-03-26T22:01:08Z","volume":3,"year":"2023","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"month":"03","publication_identifier":{"eissn":["2662-8457"]},"doi":"10.1038/s43588-023-00410-9","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2108.06686"]},"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}]},{"date_published":"2023-05-05T00:00:00Z","page":"190","citation":{"ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891."},"article_processing_charge":"No","has_accepted_license":"1","day":"05","file":[{"creator":"aschauer","content_type":"application/pdf","file_size":31434230,"access_level":"closed","file_name":"Thesis_Schauer_final.pdf","embargo_to":"open_access","checksum":"59b0303dc483f40a96a610a90aab7ee9","date_created":"2023-05-05T13:01:14Z","date_updated":"2023-05-05T13:01:14Z","embargo":"2024-05-05","file_id":"12907","relation":"main_file"},{"file_id":"12908","relation":"source_file","checksum":"25f54e12479b6adaabd129a20568e6c1","date_updated":"2023-05-05T13:04:15Z","date_created":"2023-05-05T13:04:15Z","access_level":"closed","file_name":"Thesis_Schauer_final.docx","creator":"aschauer","file_size":43809109,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12891","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"doi":"10.15479/at:ista:12891","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663 - 337X"]},"month":"05","date_updated":"2023-08-21T06:25:48Z","date_created":"2023-05-05T08:48:20Z","related_material":{"record":[{"id":"8966","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7888"}]},"author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","first_name":"Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","ec_funded":1,"file_date_updated":"2023-05-05T13:04:15Z"},{"ddc":["000"],"status":"public","title":"Efficient data structures for incremental exact and approximate maximum flow","intvolume":" 261","_id":"14085","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_size":875910,"content_type":"application/pdf","creator":"dernst","file_name":"2023_LIPIcsICALP_Goranci.pdf","access_level":"open_access","date_updated":"2023-08-21T06:59:05Z","date_created":"2023-08-21T06:59:05Z","checksum":"074177e815a1656de5d4071c7a3dffa6","success":1,"relation":"main_file","file_id":"14089"}],"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"apa":"Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69","ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","ista":"Goranci G, Henzinger MH. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 69.","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.69","chicago":"Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69."},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","date_created":"2023-08-20T22:01:14Z","date_updated":"2023-08-21T07:00:49Z","volume":261,"author":[{"full_name":"Goranci, Gramoz","last_name":"Goranci","first_name":"Gramoz"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"}],"article_number":"69","file_date_updated":"2023-08-21T06:59:05Z","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"unknown":["2211.09606"]},"language":[{"iso":"eng"}],"conference":{"location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.69","month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]}},{"month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2007.10824"]},"quality_controlled":"1","conference":{"start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.72","language":[{"iso":"eng"}],"article_number":"72","file_date_updated":"2023-08-21T06:45:16Z","year":"2023","acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"David G.","last_name":"Harris","full_name":"Harris, David G."},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-21T06:49:11Z","date_created":"2023-08-20T22:01:14Z","volume":261,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72","ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 72.","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72."},"date_published":"2023-07-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.","lang":"eng"}],"_id":"14084","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Parameter estimation for Gibbs distributions","ddc":["000","510"],"intvolume":" 261","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":917791,"file_name":"2023_LIPIcsICALP_Harris.pdf","access_level":"open_access","date_created":"2023-08-21T06:45:16Z","date_updated":"2023-08-21T06:45:16Z","success":1,"checksum":"6dee0684245bb1c524b9c955db1e933d","file_id":"14088","relation":"main_file"}]},{"ec_funded":1,"file_date_updated":"2023-08-21T07:04:36Z","article_number":"74","author":[{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"last_name":"Liu","first_name":"Paul","full_name":"Liu, Paul"},{"first_name":"Jan","last_name":"Vondrák","full_name":"Vondrák, Jan"},{"last_name":"Zheng","first_name":"Da Wei","full_name":"Zheng, Da Wei"}],"volume":261,"date_updated":"2023-08-21T07:05:47Z","date_created":"2023-08-20T22:01:14Z","year":"2023","acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"month":"07","doi":"10.4230/LIPIcs.ICALP.2023.74","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2305.00122"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"quality_controlled":"1","abstract":[{"text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"file_name":"2023_LIPIcsICALP_HenzingerM.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":930943,"file_id":"14090","relation":"main_file","date_updated":"2023-08-21T07:04:36Z","date_created":"2023-08-21T07:04:36Z","success":1,"checksum":"a5eef225014e003efbfbe4830fdd23cb"}],"_id":"14086","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 261","title":"Faster submodular maximization for several classes of matroids","status":"public","ddc":["000"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","citation":{"chicago":"Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.","short":"M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes of Matroids.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.","ieee":"M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74","ista":"Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 74.","ama":"Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74"},"publication":"50th International Colloquium on Automata, Languages, and Programming"},{"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed."}],"intvolume":" 261","status":"public","ddc":["000"],"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","_id":"14083","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"14091","date_updated":"2023-08-21T07:23:18Z","date_created":"2023-08-21T07:23:18Z","checksum":"a449143fec3fbebb092cb8ef3b53c226","success":1,"file_name":"2023_LIPIcsICALP_Resch.pdf","access_level":"open_access","file_size":1141497,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","citation":{"ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99","apa":"Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 99.","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.99.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99."},"publication":"50th International Colloquium on Automata, Languages, and Programming","date_published":"2023-07-01T00:00:00Z","article_number":"99","file_date_updated":"2023-08-21T07:23:18Z","department":[{"_id":"MaMo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2023","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","volume":261,"date_updated":"2023-08-21T07:26:01Z","date_created":"2023-08-20T22:01:13Z","author":[{"full_name":"Resch, Nicolas","first_name":"Nicolas","last_name":"Resch"},{"full_name":"Yuan, Chen","first_name":"Chen","last_name":"Yuan"},{"first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2210.07754"]},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2023.99","conference":{"end_date":"2023-07-14","start_date":"2023-07-10","location":"Paderborn, Germany","name":"ICALP: International Colloquium on Automata, Languages, and Programming"}},{"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"month":"01","main_file_link":[{"url":"https://doi.org/10.1002/anie.202211663","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1002/anie.202211663","language":[{"iso":"eng"}],"article_number":"e202211663","extern":"1","year":"2023","publisher":"Wiley","publication_status":"published","author":[{"full_name":"Lepre, Enrico","first_name":"Enrico","last_name":"Lepre"},{"last_name":"Rat","first_name":"Sylvain","full_name":"Rat, Sylvain"},{"full_name":"Cavedon, Cristian","last_name":"Cavedon","first_name":"Cristian"},{"full_name":"Seeberger, Peter H.","first_name":"Peter H.","last_name":"Seeberger"},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","last_name":"Pieber","full_name":"Pieber, Bartholomäus"},{"full_name":"Antonietti, Markus","first_name":"Markus","last_name":"Antonietti"},{"last_name":"López‐Salas","first_name":"Nieves","full_name":"López‐Salas, Nieves"}],"volume":62,"date_updated":"2023-08-21T09:18:12Z","date_created":"2023-05-08T08:28:14Z","scopus_import":"1","keyword":["General Chemistry","Catalysis"],"article_processing_charge":"No","day":"09","citation":{"chicago":"Lepre, Enrico, Sylvain Rat, Cristian Cavedon, Peter H. Seeberger, Bartholomäus Pieber, Markus Antonietti, and Nieves López‐Salas. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202211663.","short":"E. Lepre, S. Rat, C. Cavedon, P.H. Seeberger, B. Pieber, M. Antonietti, N. López‐Salas, Angewandte Chemie International Edition 62 (2023).","mla":"Lepre, Enrico, et al. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” Angewandte Chemie International Edition, vol. 62, no. 2, e202211663, Wiley, 2023, doi:10.1002/anie.202211663.","ieee":"E. Lepre et al., “Catalytic properties of high nitrogen content carbonaceous materials,” Angewandte Chemie International Edition, vol. 62, no. 2. Wiley, 2023.","apa":"Lepre, E., Rat, S., Cavedon, C., Seeberger, P. H., Pieber, B., Antonietti, M., & López‐Salas, N. (2023). Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211663","ista":"Lepre E, Rat S, Cavedon C, Seeberger PH, Pieber B, Antonietti M, López‐Salas N. 2023. Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. 62(2), e202211663.","ama":"Lepre E, Rat S, Cavedon C, et al. Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. 2023;62(2). doi:10.1002/anie.202211663"},"publication":"Angewandte Chemie International Edition","article_type":"original","date_published":"2023-01-09T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The influence of structural modifications on the catalytic activity of carbon materials is poorly understood. A collection of carbonaceous materials with different pore networks and high nitrogen content was characterized and used to catalyze four reactions to deduce structure–activity relationships. The CO2 cycloaddition and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species). The absence of large conjugated carbon domains resulting from the introduction of large amounts of nitrogen in the carbon network is responsible for poor redox activity, as observed through the catalytic reduction of nitrobenzene with hydrazine and the catalytic oxidation of 3,3′,5,5′-tetramethylbenzidine using hydroperoxide. The material with the highest activity towards Lewis acid catalysis (in the hydrolysis of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule activation and presents the highest concentration of electron-poor nitrogen species."}],"_id":"12922","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 62","status":"public","title":"Catalytic properties of high nitrogen content carbonaceous materials","oa_version":"Published Version"},{"article_number":"18","extern":"1","year":"2023","publication_status":"published","publisher":"American Astronomical Society","author":[{"full_name":"O‘Grady, Anna J. G.","last_name":"O‘Grady","first_name":"Anna J. G."},{"first_name":"Maria R.","last_name":"Drout","full_name":"Drout, Maria R."},{"first_name":"B. M.","last_name":"Gaensler","full_name":"Gaensler, B. M."},{"full_name":"Kochanek, C. S.","first_name":"C. S.","last_name":"Kochanek"},{"full_name":"Neugent, Kathryn F.","first_name":"Kathryn F.","last_name":"Neugent"},{"last_name":"Doherty","first_name":"Carolyn L.","full_name":"Doherty, Carolyn L."},{"full_name":"Speagle, Joshua S.","last_name":"Speagle","first_name":"Joshua S."},{"full_name":"Shappee, B. J.","last_name":"Shappee","first_name":"B. J."},{"first_name":"Michael","last_name":"Rauch","full_name":"Rauch, Michael"},{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"first_name":"Bethany","last_name":"Ludwig","full_name":"Ludwig, Bethany"},{"full_name":"Thompson, Todd A.","last_name":"Thompson","first_name":"Todd A."}],"date_created":"2023-08-03T10:10:12Z","date_updated":"2023-08-21T12:07:05Z","volume":943,"month":"01","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"external_id":{"arxiv":["2211.12438"]},"main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/aca655","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.3847/1538-4357/aca655","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"In previous work, we identified a population of 38 cool and luminous variable stars in the Magellanic Clouds and examined 11 in detail in order to classify them as either Thorne–Żytkow objects (TŻOs; red supergiants with a neutron star cores) or super-asymptotic giant branch (sAGB) stars (the most massive stars that will not undergo core collapse). This population includes HV 2112, a peculiar star previously considered in other works to be either a TŻO or high-mass asymptotic giant branch (AGB) star. Here we continue this investigation, using the kinematic and radio environments and local star formation history of these stars to place constraints on the age of the progenitor systems and the presence of past supernovae. These stars are not associated with regions of recent star formation, and we find no evidence of past supernovae at their locations. Finally, we also assess the presence of heavy elements and lithium in their spectra compared to red supergiants. We find strong absorption in Li and s-process elements compared to RSGs in most of the sample, consistent with sAGB nucleosynthesis, while HV 2112 shows additional strong lines associated with TŻO nucleosynthesis. Coupled with our previous mass estimates, the results are consistent with the stars being massive (∼4–6.5 M⊙) or sAGB (∼6.5–12 M⊙) stars in the thermally pulsing phase, providing crucial observations of the transition between low- and high-mass stellar populations. HV 2112 is more ambiguous; it could either be a maximally massive sAGB star, or a TŻO if the minimum mass for stability extends down to ≲13 M⊙.","lang":"eng"}],"issue":"1","_id":"13450","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates","intvolume":" 943","oa_version":"Published Version","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"20","article_processing_charge":"No","publication":"The Astrophysical Journal","citation":{"ama":"O‘Grady AJG, Drout MR, Gaensler BM, et al. Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. 2023;943(1). doi:10.3847/1538-4357/aca655","ista":"O‘Grady AJG, Drout MR, Gaensler BM, Kochanek CS, Neugent KF, Doherty CL, Speagle JS, Shappee BJ, Rauch M, Götberg YLL, Ludwig B, Thompson TA. 2023. Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. 943(1), 18.","apa":"O‘Grady, A. J. G., Drout, M. R., Gaensler, B. M., Kochanek, C. S., Neugent, K. F., Doherty, C. L., … Thompson, T. A. (2023). Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/aca655","ieee":"A. J. G. O‘Grady et al., “Cool, luminous, and highly variable stars in the Magellanic Clouds. II. Spectroscopic and environmental analysis of Thorne–Żytkow object and super-AGB star candidates,” The Astrophysical Journal, vol. 943, no. 1. American Astronomical Society, 2023.","mla":"O‘Grady, Anna J. G., et al. “Cool, Luminous, and Highly Variable Stars in the Magellanic Clouds. II. Spectroscopic and Environmental Analysis of Thorne–Żytkow Object and Super-AGB Star Candidates.” The Astrophysical Journal, vol. 943, no. 1, 18, American Astronomical Society, 2023, doi:10.3847/1538-4357/aca655.","short":"A.J.G. O‘Grady, M.R. Drout, B.M. Gaensler, C.S. Kochanek, K.F. Neugent, C.L. Doherty, J.S. Speagle, B.J. Shappee, M. Rauch, Y.L.L. Götberg, B. Ludwig, T.A. Thompson, The Astrophysical Journal 943 (2023).","chicago":"O‘Grady, Anna J. G., Maria R. Drout, B. M. Gaensler, C. S. Kochanek, Kathryn F. Neugent, Carolyn L. Doherty, Joshua S. Speagle, et al. “Cool, Luminous, and Highly Variable Stars in the Magellanic Clouds. II. Spectroscopic and Environmental Analysis of Thorne–Żytkow Object and Super-AGB Star Candidates.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/aca655."},"article_type":"original","date_published":"2023-01-20T00:00:00Z"},{"article_number":"021001","extern":"1","publication_status":"published","publisher":"IOP Publishing","year":"2023","date_created":"2023-08-03T10:09:57Z","date_updated":"2023-08-21T12:09:14Z","volume":135,"author":[{"full_name":"Geen, Sam","last_name":"Geen","first_name":"Sam"},{"full_name":"Agrawal, Poojan","first_name":"Poojan","last_name":"Agrawal"},{"full_name":"Crowther, Paul A.","last_name":"Crowther","first_name":"Paul A."},{"full_name":"Keller, B. W.","last_name":"Keller","first_name":"B. W."},{"first_name":"Alex","last_name":"de Koter","full_name":"de Koter, Alex"},{"first_name":"Zsolt","last_name":"Keszthelyi","full_name":"Keszthelyi, Zsolt"},{"first_name":"Freeke","last_name":"van de Voort","full_name":"van de Voort, Freeke"},{"full_name":"Ali, Ahmad A.","first_name":"Ahmad A.","last_name":"Ali"},{"first_name":"Frank","last_name":"Backs","full_name":"Backs, Frank"},{"last_name":"Bonne","first_name":"Lars","full_name":"Bonne, Lars"},{"last_name":"Brugaletta","first_name":"Vittoria","full_name":"Brugaletta, Vittoria"},{"full_name":"Derkink, Annelotte","last_name":"Derkink","first_name":"Annelotte"},{"full_name":"Ekström, Sylvia","last_name":"Ekström","first_name":"Sylvia"},{"full_name":"Fichtner, Yvonne A.","first_name":"Yvonne A.","last_name":"Fichtner"},{"last_name":"Grassitelli","first_name":"Luca","full_name":"Grassitelli, Luca"},{"full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"Erin R.","last_name":"Higgins","full_name":"Higgins, Erin R."},{"first_name":"Eva","last_name":"Laplace","full_name":"Laplace, Eva"},{"full_name":"You Liow, Kong","last_name":"You Liow","first_name":"Kong"},{"first_name":"Marta","last_name":"Lorenzo","full_name":"Lorenzo, Marta"},{"full_name":"McLeod, Anna F.","last_name":"McLeod","first_name":"Anna F."},{"first_name":"Georges","last_name":"Meynet","full_name":"Meynet, Georges"},{"first_name":"Megan","last_name":"Newsome","full_name":"Newsome, Megan"},{"full_name":"André Oliva, G.","last_name":"André Oliva","first_name":"G."},{"full_name":"Ramachandran, Varsha","last_name":"Ramachandran","first_name":"Varsha"},{"first_name":"Martin P.","last_name":"Rey","full_name":"Rey, Martin P."},{"full_name":"Rieder, Steven","last_name":"Rieder","first_name":"Steven"},{"last_name":"Romano-Díaz","first_name":"Emilio","full_name":"Romano-Díaz, Emilio"},{"first_name":"Gautham","last_name":"Sabhahit","full_name":"Sabhahit, Gautham"},{"first_name":"Andreas A. C.","last_name":"Sander","full_name":"Sander, Andreas A. C."},{"last_name":"Sarwar","first_name":"Rafia","full_name":"Sarwar, Rafia"},{"last_name":"Stinshoff","first_name":"Hanno","full_name":"Stinshoff, Hanno"},{"full_name":"Stoop, Mitchel","last_name":"Stoop","first_name":"Mitchel"},{"first_name":"Dorottya","last_name":"Szécsi","full_name":"Szécsi, Dorottya"},{"first_name":"Maxime","last_name":"Trebitsch","full_name":"Trebitsch, Maxime"},{"full_name":"Vink, Jorick S.","last_name":"Vink","first_name":"Jorick S."},{"last_name":"Winch","first_name":"Ethan","full_name":"Winch, Ethan"}],"month":"03","publication_identifier":{"issn":["0004-6280"],"eissn":["1538-3873"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1538-3873/acb6b5"}],"external_id":{"arxiv":["2301.13611"]},"language":[{"iso":"eng"}],"doi":"10.1088/1538-3873/acb6b5","type":"journal_article","abstract":[{"lang":"eng","text":"Stars strongly impact their environment, and shape structures on all scales throughout the universe, in a process known as \"feedback.\" Due to the complexity of both stellar evolution and the physics of larger astrophysical structures, there remain many unanswered questions about how feedback operates and what we can learn about stars by studying their imprint on the wider universe. In this white paper, we summarize discussions from the Lorentz Center meeting \"Bringing Stellar Evolution and Feedback Together\" in 2022 April and identify key areas where further dialog can bring about radical changes in how we view the relationship between stars and the universe they live in."}],"issue":"1044","title":"Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop","status":"public","intvolume":" 135","_id":"13449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","day":"09","article_processing_charge":"No","article_type":"original","publication":"Publications of the Astronomical Society of the Pacific","citation":{"ista":"Geen S, Agrawal P, Crowther PA, Keller BW, de Koter A, Keszthelyi Z, van de Voort F, Ali AA, Backs F, Bonne L, Brugaletta V, Derkink A, Ekström S, Fichtner YA, Grassitelli L, Götberg YLL, Higgins ER, Laplace E, You Liow K, Lorenzo M, McLeod AF, Meynet G, Newsome M, André Oliva G, Ramachandran V, Rey MP, Rieder S, Romano-Díaz E, Sabhahit G, Sander AAC, Sarwar R, Stinshoff H, Stoop M, Szécsi D, Trebitsch M, Vink JS, Winch E. 2023. Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. 135(1044), 021001.","apa":"Geen, S., Agrawal, P., Crowther, P. A., Keller, B. W., de Koter, A., Keszthelyi, Z., … Winch, E. (2023). Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/acb6b5","ieee":"S. Geen et al., “Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop,” Publications of the Astronomical Society of the Pacific, vol. 135, no. 1044. IOP Publishing, 2023.","ama":"Geen S, Agrawal P, Crowther PA, et al. Bringing stellar evolution and feedback together: Summary of proposals from the Lorentz Center workshop. Publications of the Astronomical Society of the Pacific. 2023;135(1044). doi:10.1088/1538-3873/acb6b5","chicago":"Geen, Sam, Poojan Agrawal, Paul A. Crowther, B. W. Keller, Alex de Koter, Zsolt Keszthelyi, Freeke van de Voort, et al. “Bringing Stellar Evolution and Feedback Together: Summary of Proposals from the Lorentz Center Workshop.” Publications of the Astronomical Society of the Pacific. IOP Publishing, 2023. https://doi.org/10.1088/1538-3873/acb6b5.","mla":"Geen, Sam, et al. “Bringing Stellar Evolution and Feedback Together: Summary of Proposals from the Lorentz Center Workshop.” Publications of the Astronomical Society of the Pacific, vol. 135, no. 1044, 021001, IOP Publishing, 2023, doi:10.1088/1538-3873/acb6b5.","short":"S. Geen, P. Agrawal, P.A. Crowther, B.W. Keller, A. de Koter, Z. Keszthelyi, F. van de Voort, A.A. Ali, F. Backs, L. Bonne, V. Brugaletta, A. Derkink, S. Ekström, Y.A. Fichtner, L. Grassitelli, Y.L.L. Götberg, E.R. Higgins, E. Laplace, K. You Liow, M. Lorenzo, A.F. McLeod, G. Meynet, M. Newsome, G. André Oliva, V. Ramachandran, M.P. Rey, S. Rieder, E. Romano-Díaz, G. Sabhahit, A.A.C. Sander, R. Sarwar, H. Stinshoff, M. Stoop, D. Szécsi, M. Trebitsch, J.S. Vink, E. Winch, Publications of the Astronomical Society of the Pacific 135 (2023)."},"date_published":"2023-03-09T00:00:00Z"},{"publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. 2023;524(2):1692-1709. doi:10.1093/mnras/stad1977","ista":"Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. 2023. Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. 524(2), 1692–1709.","apa":"Farmer, R., Renzo, M., Götberg, Y. L. L., Bellinger, E., Justham, S., & de Mink, S. E. (2023). Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad1977","ieee":"R. Farmer, M. Renzo, Y. L. L. Götberg, E. Bellinger, S. Justham, and S. E. de Mink, “Observational predictions for Thorne–Żytkow objects,” Monthly Notices of the Royal Astronomical Society, vol. 524, no. 2. Oxford University Press, pp. 1692–1709, 2023.","mla":"Farmer, R., et al. “Observational Predictions for Thorne–Żytkow Objects.” Monthly Notices of the Royal Astronomical Society, vol. 524, no. 2, Oxford University Press, 2023, pp. 1692–709, doi:10.1093/mnras/stad1977.","short":"R. Farmer, M. Renzo, Y.L.L. Götberg, E. Bellinger, S. Justham, S.E. de Mink, Monthly Notices of the Royal Astronomical Society 524 (2023) 1692–1709.","chicago":"Farmer, R, M Renzo, Ylva Louise Linsdotter Götberg, E Bellinger, S Justham, and S E de Mink. “Observational Predictions for Thorne–Żytkow Objects.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2023. https://doi.org/10.1093/mnras/stad1977."},"article_type":"original","page":"1692-1709","date_published":"2023-09-01T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14104","title":"Observational predictions for Thorne–Żytkow objects","status":"public","intvolume":" 524","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Thorne–Żytkow objects (TŻO) are potential end products of the merger of a neutron star with a non-degenerate star. In this work, we have computed the first grid of evolutionary models of TŻOs with the MESA stellar evolution code. With these models, we predict several observational properties of TŻOs, including their surface temperatures and luminosities, pulsation periods, and nucleosynthetic products. We expand the range of possible TŻO solutions to cover 3.45≲log(Teff/K)≲3.65 and 4.85≲log(L/L⊙)≲5.5. Due to the much higher densities our TŻOs reach compared to previous models, if TŻOs form we expect them to be stable over a larger mass range than previously predicted, without exhibiting a gap in their mass distribution. Using the GYRE stellar pulsation code we show that TŻOs should have fundamental pulsation periods of 1000–2000 d, and period ratios of ≈0.2–0.3. Models computed with a large 399 isotope fully coupled nuclear network show a nucleosynthetic signal that is different to previously predicted. We propose a new nucleosynthetic signal to determine a star’s status as a TŻO: the isotopologues 44TiO2 and 44TiO, which will have a shift in their spectral features as compared to stable titanium-containing molecules. We find that in the local Universe (∼SMC metallicities and above) TŻOs show little heavy metal enrichment, potentially explaining the difficulty in finding TŻOs to-date."}],"issue":"2","external_id":{"arxiv":["2305.07337"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2305.07337"}],"quality_controlled":"1","doi":"10.1093/mnras/stad1977","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"year":"2023","publication_status":"published","publisher":"Oxford University Press","author":[{"full_name":"Farmer, R","last_name":"Farmer","first_name":"R"},{"first_name":"M","last_name":"Renzo","full_name":"Renzo, M"},{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"last_name":"Bellinger","first_name":"E","full_name":"Bellinger, E"},{"first_name":"S","last_name":"Justham","full_name":"Justham, S"},{"full_name":"de Mink, S E","first_name":"S E","last_name":"de Mink"}],"date_updated":"2023-08-21T12:12:48Z","date_created":"2023-08-21T10:13:56Z","volume":524,"extern":"1"},{"date_created":"2023-08-09T13:06:59Z","date_updated":"2023-08-22T06:50:04Z","volume":14,"author":[{"full_name":"Hales, Jordyn","last_name":"Hales","first_name":"Jordyn"},{"full_name":"Bajpai, Utkarsh","first_name":"Utkarsh","last_name":"Bajpai"},{"full_name":"Liu, Tongtong","first_name":"Tongtong","last_name":"Liu"},{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Li","first_name":"Mingda","full_name":"Li, Mingda"},{"full_name":"Mitrano, Matteo","first_name":"Matteo","last_name":"Mitrano"},{"first_name":"Yao","last_name":"Wang","full_name":"Wang, Yao"}],"publication_status":"published","publisher":"Springer Nature","year":"2023","pmid":1,"extern":"1","article_number":"3512","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-38540-3","quality_controlled":"1","oa":1,"external_id":{"pmid":["37316515"],"arxiv":["2209.02283"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"month":"06","publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","status":"public","intvolume":" 14","_id":"13989","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements."}],"type":"journal_article","date_published":"2023-06-14T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., & Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38540-3","ieee":"J. Hales et al., “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 2023;14. doi:10.1038/s41467-023-38540-3","chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38540-3.","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” Nature Communications, vol. 14, 3512, Springer Nature, 2023, doi:10.1038/s41467-023-38540-3.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023)."},"day":"14","article_processing_charge":"No","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"scopus_import":"1"},{"extern":"1","article_number":"106902","volume":130,"date_updated":"2023-08-22T07:18:01Z","date_created":"2023-08-09T13:07:24Z","author":[{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"full_name":"Kalthoff, Mona H.","last_name":"Kalthoff","first_name":"Mona H."},{"first_name":"Damian","last_name":"Hofmann","full_name":"Hofmann, Damian"},{"last_name":"Claassen","first_name":"Martin","full_name":"Claassen, Martin"},{"full_name":"Kennes, Dante M.","last_name":"Kennes","first_name":"Dante M."},{"full_name":"Sentef, Michael A.","first_name":"Michael A.","last_name":"Sentef"},{"first_name":"Matteo","last_name":"Mitrano","full_name":"Mitrano, Matteo"}],"publisher":"American Physical Society","publication_status":"published","pmid":1,"year":"2023","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.106902","quality_controlled":"1","oa":1,"external_id":{"pmid":["36962013"],"arxiv":["2209.02081"]},"main_file_link":[{"url":"https://arxiv.org/abs/2209.02081","open_access":"1"}],"issue":"10","abstract":[{"lang":"eng","text":"Many-body entanglement in condensed matter systems can be diagnosed from equilibrium response functions through the use of entanglement witnesses and operator-specific quantum bounds. Here, we investigate the applicability of this approach for detecting entangled states in quantum systems driven out of equilibrium. We use a multipartite entanglement witness, the quantum Fisher information, to study the dynamics of a paradigmatic fermion chain undergoing a time-dependent change of the Coulomb interaction. Our results show that the quantum Fisher information is able to witness distinct signatures of multipartite entanglement both near and far from equilibrium that are robust against decoherence. We discuss implications of these findings for probing entanglement in light-driven quantum materials with time-resolved optical and x-ray scattering methods."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 130","status":"public","title":"Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13990","article_processing_charge":"No","day":"10","keyword":["General Physics and Astronomy"],"scopus_import":"1","date_published":"2023-03-10T00:00:00Z","article_type":"original","citation":{"mla":"Baykusheva, Denitsa Rangelova, et al. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” Physical Review Letters, vol. 130, no. 10, 106902, American Physical Society, 2023, doi:10.1103/physrevlett.130.106902.","short":"D.R. Baykusheva, M.H. Kalthoff, D. Hofmann, M. Claassen, D.M. Kennes, M.A. Sentef, M. Mitrano, Physical Review Letters 130 (2023).","chicago":"Baykusheva, Denitsa Rangelova, Mona H. Kalthoff, Damian Hofmann, Martin Claassen, Dante M. Kennes, Michael A. Sentef, and Matteo Mitrano. “Witnessing Nonequilibrium Entanglement Dynamics in a Strongly Correlated Fermionic Chain.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106902.","ama":"Baykusheva DR, Kalthoff MH, Hofmann D, et al. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106902","ista":"Baykusheva DR, Kalthoff MH, Hofmann D, Claassen M, Kennes DM, Sentef MA, Mitrano M. 2023. Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. 130(10), 106902.","apa":"Baykusheva, D. R., Kalthoff, M. H., Hofmann, D., Claassen, M., Kennes, D. M., Sentef, M. A., & Mitrano, M. (2023). Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106902","ieee":"D. R. Baykusheva et al., “Witnessing nonequilibrium entanglement dynamics in a strongly correlated fermionic chain,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023."},"publication":"Physical Review Letters"},{"doi":"10.1103/physrevlett.130.098202","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.02488"],"isi":["000946178200008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2211.02488"}],"project":[{"grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"03","related_material":{"record":[{"status":"public","relation":"research_paper","id":"8101"}]},"author":[{"orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean","first_name":"Galien M","full_name":"Grosjean, Galien M"},{"last_name":"Waitukaitis","first_name":"Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R"}],"volume":130,"date_updated":"2023-08-22T08:41:32Z","date_created":"2023-02-28T12:14:46Z","acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","year":"2023","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","publication_status":"published","ec_funded":1,"file_date_updated":"2023-02-28T12:37:54Z","article_number":"098202","date_published":"2023-03-03T00:00:00Z","citation":{"ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202.","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” Physical Review Letters, vol. 130, no. 9. American Physical Society, 2023.","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.098202","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:10.1103/physrevlett.130.098202.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.098202."},"publication":"Physical Review Letters","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"03","keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"oa_version":"Preprint","file":[{"relation":"main_file","file_id":"12698","checksum":"c4f2f6eea0408811f8f4898e15890355","success":1,"date_updated":"2023-02-28T12:20:27Z","date_created":"2023-02-28T12:20:27Z","access_level":"open_access","file_name":"Main_Preprint.pdf","content_type":"application/pdf","file_size":2301864,"creator":"ggrosjea"},{"file_id":"12699","relation":"main_file","success":1,"checksum":"6af6ed6c97a977f923de4162294b43c4","date_updated":"2023-02-28T12:20:55Z","date_created":"2023-02-28T12:20:55Z","access_level":"open_access","file_name":"Suppl_info.pdf","creator":"ggrosjea","file_size":1138625,"content_type":"application/pdf"},{"creator":"ggrosjea","file_size":793449,"content_type":"video/mp4","access_level":"open_access","file_name":"Suppl_vid1.mp4","success":1,"checksum":"3f20365fb9515bdba3a111d912c8d8b4","date_updated":"2023-02-28T12:37:54Z","date_created":"2023-02-28T12:37:54Z","file_id":"12700","relation":"main_file"},{"content_type":"video/mp4","file_size":455925,"creator":"ggrosjea","file_name":"Suppl_vid2.mp4","access_level":"open_access","date_created":"2023-02-28T12:37:54Z","date_updated":"2023-02-28T12:37:54Z","checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","success":1,"relation":"main_file","file_id":"12701"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12697","intvolume":" 130","status":"public","ddc":["530","537"],"title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","issue":"9","abstract":[{"lang":"eng","text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process."}],"type":"journal_article"},{"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_processing_charge":"No","day":"01","citation":{"ieee":"J. S. Vink et al., “X-shooting ULLYSES: Massive stars at low metallicity. I. Project description,” Astronomy & Astrophysics, vol. 675. EDP Sciences, 2023.","apa":"Vink, J. S., Mehner, A., Crowther, P. A., Fullerton, A., Garcia, M., Martins, F., … Wang, L. (2023). X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202245650","ista":"Vink JS, Mehner A, Crowther PA, Fullerton A, Garcia M, Martins F, Morrell N, Oskinova LM, St-Louis N, ud-Doula A, Sander AAC, Sana H, Bouret J-C, Kubátová B, Marchant P, Martins LP, Wofford A, van Loon JT, Grace Telford O, Götberg YLL, Bowman DM, Erba C, Kalari VM, Abdul-Masih M, Alkousa T, Backs F, Barbosa CL, Berlanas SR, Bernini-Peron M, Bestenlehner JM, Blomme R, Bodensteiner J, Brands SA, Evans CJ, David-Uraz A, Driessen FA, Dsilva K, Geen S, Gómez-González VMA, Grassitelli L, Hamann W-R, Hawcroft C, Herrero A, Higgins ER, John Hillier D, Ignace R, Istrate AG, Kaper L, Kee ND, Kehrig C, Keszthelyi Z, Klencki J, de Koter A, Kuiper R, Laplace E, Larkin CJK, Lefever RR, Leitherer C, Lennon DJ, Mahy L, Maíz Apellániz J, Maravelias G, Marcolino W, McLeod AF, de Mink SE, Najarro F, Oey MS, Parsons TN, Pauli D, Pedersen MG, Prinja RK, Ramachandran V, Ramírez-Tannus MC, Sabhahit GN, Schootemeijer A, Reyero Serantes S, Shenar T, Stringfellow GS, Sudnik N, Tramper F, Wang L. 2023. X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. 675, A154.","ama":"Vink JS, Mehner A, Crowther PA, et al. X-shooting ULLYSES: Massive stars at low metallicity. I. Project description. Astronomy & Astrophysics. 2023;675. doi:10.1051/0004-6361/202245650","chicago":"Vink, Jorick S., A. Mehner, P. A. Crowther, A. Fullerton, M. Garcia, F. Martins, N. Morrell, et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity. I. Project Description.” Astronomy & Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202245650.","short":"J.S. Vink, A. Mehner, P.A. Crowther, A. Fullerton, M. Garcia, F. Martins, N. Morrell, L.M. Oskinova, N. St-Louis, A. ud-Doula, A.A.C. Sander, H. Sana, J.-C. Bouret, B. Kubátová, P. Marchant, L.P. Martins, A. Wofford, J.T. van Loon, O. Grace Telford, Y.L.L. Götberg, D.M. Bowman, C. Erba, V.M. Kalari, M. Abdul-Masih, T. Alkousa, F. Backs, C.L. Barbosa, S.R. Berlanas, M. Bernini-Peron, J.M. Bestenlehner, R. Blomme, J. Bodensteiner, S.A. Brands, C.J. Evans, A. David-Uraz, F.A. Driessen, K. Dsilva, S. Geen, V.M.A. Gómez-González, L. Grassitelli, W.-R. Hamann, C. Hawcroft, A. Herrero, E.R. Higgins, D. John Hillier, R. Ignace, A.G. Istrate, L. Kaper, N.D. Kee, C. Kehrig, Z. Keszthelyi, J. Klencki, A. de Koter, R. Kuiper, E. Laplace, C.J.K. Larkin, R.R. Lefever, C. Leitherer, D.J. Lennon, L. Mahy, J. Maíz Apellániz, G. Maravelias, W. Marcolino, A.F. McLeod, S.E. de Mink, F. Najarro, M.S. Oey, T.N. Parsons, D. Pauli, M.G. Pedersen, R.K. Prinja, V. Ramachandran, M.C. Ramírez-Tannus, G.N. Sabhahit, A. Schootemeijer, S. Reyero Serantes, T. Shenar, G.S. Stringfellow, N. Sudnik, F. Tramper, L. Wang, Astronomy & Astrophysics 675 (2023).","mla":"Vink, Jorick S., et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity. I. Project Description.” Astronomy & Astrophysics, vol. 675, A154, EDP Sciences, 2023, doi:10.1051/0004-6361/202245650."},"publication":"Astronomy & Astrophysics","article_type":"original","date_published":"2023-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Observations of individual massive stars, super-luminous supernovae, gamma-ray bursts, and gravitational wave events involving spectacular black hole mergers indicate that the low-metallicity Universe is fundamentally different from our own Galaxy. Many transient phenomena will remain enigmatic until we achieve a firm understanding of the physics and evolution of massive stars at low metallicity (Z). The Hubble Space Telescope has devoted 500 orbits to observing ∼250 massive stars at low Z in the ultraviolet (UV) with the COS and STIS spectrographs under the ULLYSES programme. The complementary X-Shooting ULLYSES (XShootU) project provides an enhanced legacy value with high-quality optical and near-infrared spectra obtained with the wide-wavelength coverage X-shooter spectrograph at ESO’s Very Large Telescope. We present an overview of the XShootU project, showing that combining ULLYSES UV and XShootU optical spectra is critical for the uniform determination of stellar parameters such as effective temperature, surface gravity, luminosity, and abundances, as well as wind properties such as mass-loss rates as a function of Z. As uncertainties in stellar and wind parameters percolate into many adjacent areas of astrophysics, the data and modelling of the XShootU project is expected to be a game changer for our physical understanding of massive stars at low Z. To be able to confidently interpret James Webb Space Telescope spectra of the first stellar generations, the individual spectra of low-Z stars need to be understood, which is exactly where XShootU can deliver.","lang":"eng"}],"_id":"14103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 675","title":"X-shooting ULLYSES: Massive stars at low metallicity. I. Project description","status":"public","oa_version":"Published Version","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"07","oa":1,"external_id":{"arxiv":["2305.06376"]},"main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/202245650","open_access":"1"}],"quality_controlled":"1","doi":"10.1051/0004-6361/202245650","language":[{"iso":"eng"}],"article_number":"A154","extern":"1","year":"2023","publisher":"EDP Sciences","publication_status":"published","author":[{"last_name":"Vink","first_name":"Jorick S.","full_name":"Vink, Jorick S."},{"first_name":"A.","last_name":"Mehner","full_name":"Mehner, A."},{"last_name":"Crowther","first_name":"P. A.","full_name":"Crowther, P. 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P.","last_name":"Martins"},{"last_name":"Wofford","first_name":"A.","full_name":"Wofford, A."},{"first_name":"J. Th.","last_name":"van Loon","full_name":"van Loon, J. Th."},{"full_name":"Grace Telford, O.","last_name":"Grace Telford","first_name":"O."},{"orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter"},{"full_name":"Bowman, D. M.","first_name":"D. M.","last_name":"Bowman"},{"first_name":"C.","last_name":"Erba","full_name":"Erba, C."},{"first_name":"V. M.","last_name":"Kalari","full_name":"Kalari, V. M."},{"full_name":"Abdul-Masih, M.","first_name":"M.","last_name":"Abdul-Masih"},{"full_name":"Alkousa, T.","first_name":"T.","last_name":"Alkousa"},{"full_name":"Backs, F.","first_name":"F.","last_name":"Backs"},{"last_name":"Barbosa","first_name":"C. L.","full_name":"Barbosa, C. L."},{"first_name":"S. R.","last_name":"Berlanas","full_name":"Berlanas, S. 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We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. 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We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-05-05T00:00:00Z","citation":{"ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900","ama":"Sahu R. 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Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023."},"page":"190","day":"05","has_accepted_license":"1","article_processing_charge":"No","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"author":[{"last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"}],"related_material":{"record":[{"relation":"new_edition","status":"public","id":"13175"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9114"}]},"date_updated":"2023-08-24T11:16:35Z","date_created":"2023-05-05T11:08:50Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"file_date_updated":"2023-07-06T11:37:40Z","ec_funded":1,"doi":"10.15479/at:ista:12900","supervisor":[{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"month":"05","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]}},{"oa_version":"Preprint","title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","status":"public","intvolume":" 37","_id":"14242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs.","lang":"eng"}],"issue":"12","type":"conference","date_published":"2023-06-26T00:00:00Z","page":"14964-14973","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","citation":{"short":"M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–14973.","mla":"Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.","chicago":"Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger, and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:14964–73. Association for the Advancement of Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.","ama":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973. doi:10.1609/aaai.v37i12.26747","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747","ista":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 14964–14973."},"day":"26","article_processing_charge":"No","scopus_import":"1","date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:06:14Z","volume":37,"author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"}],"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research was sponsored by the United\r\nStates Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied,\r\nof the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright\r\nnotation herein. The research was also funded in part by the AI2050 program at Schmidt Futures (Grant G-22-63172) and Capgemini SE.","year":"2023","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2023-02-07","location":"Washington, DC, United States","end_date":"2023-02-14","name":"AAAI: Conference on Artificial Intelligence"},"doi":"10.1609/aaai.v37i12.26747","quality_controlled":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"external_id":{"arxiv":["2211.16187"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.16187"}],"month":"06","publication_identifier":{"isbn":["9781577358800"]}},{"article_processing_charge":"No","day":"27","scopus_import":"1","date_published":"2023-06-27T00:00:00Z","citation":{"chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, pp. 5464–5471.","ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","apa":"Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States. https://doi.org/10.1609/aaai.v37i5.25679","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679"},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","page":"5464-5471","issue":"5","abstract":[{"text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games.","lang":"eng"}],"type":"conference","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14243","intvolume":" 37","status":"public","title":"Bidding graph games with partially-observable budgets","publication_identifier":{"isbn":["9781577358800"]},"month":"06","doi":"10.1609/aaai.v37i5.25679","conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14","start_date":"2023-02-07","location":"Washington, DC, United States"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1609/aaai.v37i5.25679","open_access":"1"}],"external_id":{"arxiv":["2211.13626"]},"oa":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","ec_funded":1,"author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jecker, Ismael R","first_name":"Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"volume":37,"date_updated":"2023-09-05T08:37:00Z","date_created":"2023-08-27T22:01:18Z","year":"2023","acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published"},{"status":"public","title":"Stealth shaper: Reflectivity optimization as surface stylization","_id":"14241","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects."}],"citation":{"ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20.","apa":"Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591542","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings, Los Angeles, CA, United States, 2023.","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591542","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.","mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023."},"publication":"SIGGRAPH 2023 Conference Proceedings","date_published":"2023-07-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"23","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2023","acknowledgement":"The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n","date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:22:03Z","author":[{"last_name":"Tojo","first_name":"Kenji","full_name":"Tojo, Kenji"},{"full_name":"Shamir, Ariel","last_name":"Shamir","first_name":"Ariel"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"}],"article_number":"20","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.05944","open_access":"1"}],"external_id":{"arxiv":["2305.05944"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3588432.3591542","conference":{"start_date":"2023-08-06","location":"Los Angeles, CA, United States","end_date":"2023-08-10","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"publication_identifier":{"isbn":["9798400701597"]},"month":"07"},{"external_id":{"pmid":["36695533"],"isi":["000957721600001"]},"isi":1,"quality_controlled":"1","doi":"10.1152/jn.00172.2022","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]},"month":"03","pmid":1,"acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","year":"2023","publisher":"American Physiological Society","department":[{"_id":"SiHi"}],"publication_status":"published","author":[{"last_name":"Ladle","first_name":"David R.","full_name":"Ladle, David R."},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"volume":129,"date_created":"2023-02-15T14:46:14Z","date_updated":"2023-09-05T12:13:34Z","citation":{"short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022.","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","apa":"Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512."},"publication":"Journal of Neurophysiology","page":"501-512","article_type":"original","date_published":"2023-03-01T00:00:00Z","keyword":["Physiology","General Neuroscience"],"article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12562","intvolume":" 129","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","status":"public","oa_version":"None","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons."}]},{"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"18","date_published":"2023-07-18T00:00:00Z","citation":{"ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382."},"publication":"Computer Aided Verification","page":"358–382","abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"type":"conference","alternative_title":["LNCS"],"file":[{"access_level":"open_access","file_name":"2023_LNCS_CAV_HenzingerT.pdf","content_type":"application/pdf","file_size":647760,"creator":"dernst","relation":"main_file","file_id":"13327","checksum":"ccaf94bf7d658ba012c016e11869b54c","success":1,"date_created":"2023-07-31T08:11:20Z","date_updated":"2023-07-31T08:11:20Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"13310","intvolume":" 13965","ddc":["000"],"status":"public","title":"Monitoring algorithmic fairness","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031377037"],"eissn":["1611-3349"],"isbn":["9783031377020"]},"month":"07","doi":"10.1007/978-3-031-37703-7_17","conference":{"name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2305.15979"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-07-31T08:11:20Z","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","orcid":"0009-0005-0820-1696","first_name":"Mahyar","last_name":"Karimi","full_name":"Karimi, Mahyar"},{"full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","orcid":"0000-0001-8974-2542","first_name":"Konstantin","last_name":"Kueffner"},{"full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik","first_name":"Kaushik"}],"volume":13965,"date_updated":"2023-09-05T15:14:00Z","date_created":"2023-07-25T18:32:40Z","year":"2023","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published"},{"_id":"12205","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["610"],"status":"public","title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","intvolume":" 30","file":[{"date_created":"2023-02-02T13:01:20Z","date_updated":"2023-02-02T13:01:20Z","checksum":"36a1200e1011f4b2155a8041d0308f34","success":1,"relation":"main_file","file_id":"12490","file_size":365865,"content_type":"application/pdf","creator":"dernst","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC.","lang":"eng"}],"publication":"Annals of Surgical Oncology","citation":{"mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023."},"article_type":"original","page":"35-45","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","keyword":["Oncology","Surgery"],"day":"01","has_accepted_license":"1","article_processing_charge":"No","year":"2023","acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","author":[{"first_name":"Jacek","last_name":"Glajzer","full_name":"Glajzer, Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","last_name":"Castillo-Tong","first_name":"Dan Cacsire"},{"full_name":"Richter, Rolf","last_name":"Richter","first_name":"Rolf"},{"last_name":"Vergote","first_name":"Ignace","full_name":"Vergote, Ignace"},{"full_name":"Kulbe, Hagen","first_name":"Hagen","last_name":"Kulbe"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"last_name":"Ruscito","first_name":"Ilary","full_name":"Ruscito, Ilary"},{"last_name":"Trillsch","first_name":"Fabian","full_name":"Trillsch, Fabian"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"full_name":"Gabra, Hani","last_name":"Gabra","first_name":"Hani"},{"first_name":"Eliane T.","last_name":"Taube","full_name":"Taube, Eliane T."},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"first_name":"David","last_name":"Horst","full_name":"Horst, David"},{"last_name":"Keunecke","first_name":"Carlotta","full_name":"Keunecke, Carlotta"},{"last_name":"Baum","first_name":"Joanna","full_name":"Baum, Joanna"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"full_name":"Sehouli, Jalid","last_name":"Sehouli","first_name":"Jalid"},{"first_name":"Elena Ioana","last_name":"Braicu","full_name":"Braicu, Elena Ioana"}],"related_material":{"record":[{"id":"12115","relation":"other","status":"public"}]},"date_created":"2023-01-16T09:44:36Z","date_updated":"2023-09-05T15:18:37Z","volume":30,"file_date_updated":"2023-02-02T13:01:20Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000852125500006"]},"quality_controlled":"1","isi":1,"doi":"10.1245/s10434-022-12459-3","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]}},{"scopus_import":"1","keyword":["Oncology","Surgery"],"day":"01","article_processing_charge":"No","publication":"Annals of Surgical Oncology","citation":{"ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z."},"article_type":"original","page":"46-47","date_published":"2023-01-01T00:00:00Z","type":"journal_article","_id":"12115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","intvolume":" 30","oa_version":"Published Version","month":"01","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"external_id":{"isi":["000879151800001"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1245/s10434-022-12681-z","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","year":"2023","publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"Springer Nature","author":[{"full_name":"Glajzer, Jacek","last_name":"Glajzer","first_name":"Jacek"},{"full_name":"Castillo-Tong, Dan Cacsire","first_name":"Dan Cacsire","last_name":"Castillo-Tong"},{"last_name":"Richter","first_name":"Rolf","full_name":"Richter, Rolf"},{"full_name":"Vergote, Ignace","first_name":"Ignace","last_name":"Vergote"},{"full_name":"Kulbe, Hagen","first_name":"Hagen","last_name":"Kulbe"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"full_name":"Ruscito, Ilary","first_name":"Ilary","last_name":"Ruscito"},{"full_name":"Trillsch, Fabian","first_name":"Fabian","last_name":"Trillsch"},{"full_name":"Mustea, Alexander","last_name":"Mustea","first_name":"Alexander"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"},{"full_name":"Gourley, Charlie","first_name":"Charlie","last_name":"Gourley"},{"last_name":"Gabra","first_name":"Hani","full_name":"Gabra, Hani"},{"first_name":"Eliane T.","last_name":"Taube","full_name":"Taube, Eliane T."},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"full_name":"Horst, David","last_name":"Horst","first_name":"David"},{"last_name":"Keunecke","first_name":"Carlotta","full_name":"Keunecke, Carlotta"},{"first_name":"Joanna","last_name":"Baum","full_name":"Baum, Joanna"},{"full_name":"Angelotti, Timothy","last_name":"Angelotti","first_name":"Timothy"},{"last_name":"Sehouli","first_name":"Jalid","full_name":"Sehouli, Jalid"},{"first_name":"Elena Ioana","last_name":"Braicu","full_name":"Braicu, Elena Ioana"}],"related_material":{"record":[{"status":"public","relation":"other","id":"12205"}]},"date_updated":"2023-09-05T15:18:36Z","date_created":"2023-01-12T11:56:22Z","volume":30},{"has_accepted_license":"1","article_processing_charge":"Yes","day":"26","scopus_import":"1","date_published":"2023-08-26T00:00:00Z","citation":{"apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40930-6","ieee":"N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 2023;14. doi:10.1038/s41467-023-40930-6","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231, Springer Nature, 2023, doi:10.1038/s41467-023-40930-6."},"publication":"Nature Communications","article_type":"original","abstract":[{"lang":"eng","text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Vierra.pdf","file_size":9412549,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14270","checksum":"6ab8aab4e957f626a09a1c73db3388fb","success":1,"date_created":"2023-09-06T06:50:07Z","date_updated":"2023-09-06T06:50:07Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14253","intvolume":" 14","ddc":["570"],"status":"public","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","publication_identifier":{"eissn":["2041-1723"]},"month":"08","doi":"10.1038/s41467-023-40930-6","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37633939"]},"quality_controlled":"1","file_date_updated":"2023-09-06T06:50:07Z","article_number":"5231","author":[{"full_name":"Vierra, Nicholas C.","last_name":"Vierra","first_name":"Nicholas C."},{"last_name":"Ribeiro-Silva","first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa"},{"last_name":"Kirmiz","first_name":"Michael","full_name":"Kirmiz, Michael"},{"first_name":"Deborah","last_name":"Van Der List","full_name":"Van Der List, Deborah"},{"orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","first_name":"Pradeep","full_name":"Bhandari, Pradeep"},{"full_name":"Mack, Olivia A.","last_name":"Mack","first_name":"Olivia A."},{"last_name":"Carroll","first_name":"James","full_name":"Carroll, James"},{"full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aicher, Sue A.","first_name":"Sue A.","last_name":"Aicher"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"full_name":"Trimmer, James S.","first_name":"James S.","last_name":"Trimmer"}],"volume":14,"date_created":"2023-09-03T22:01:14Z","date_updated":"2023-09-06T06:53:32Z","pmid":1,"acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","year":"2023","publisher":"Springer Nature","department":[{"_id":"RySh"}],"publication_status":"published"},{"month":"07","publication_identifier":{"isbn":["9783031377051"],"eissn":["1611-3349"],"issn":["0302-9743"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","conference":{"name":"CAV: Computer Aided Verification","end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France"},"doi":"10.1007/978-3-031-37706-8_20","language":[{"iso":"eng"}],"file_date_updated":"2023-09-06T08:25:50Z","year":"2023","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"full_name":"Prokop, Maximilian","first_name":"Maximilian","last_name":"Prokop"},{"first_name":"Sabine","last_name":"Rieder","full_name":"Rieder, Sabine"}],"date_updated":"2023-09-06T08:27:33Z","date_created":"2023-09-03T22:01:16Z","volume":13964,"scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"35th International Conference on Computer Aided Verification ","citation":{"apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th International Conference on Computer Aided Verification , 13964:390–414. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20."},"page":"390-414","date_published":"2023-07-17T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14259","title":"Guessing winning policies in LTL synthesis by semantic learning","ddc":["000"],"status":"public","intvolume":" 13964","oa_version":"Published Version","file":[{"date_created":"2023-09-06T08:25:50Z","date_updated":"2023-09-06T08:25:50Z","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","file_id":"14276","relation":"main_file","creator":"dernst","file_size":428354,"content_type":"application/pdf","file_name":"2023_LNCS_CAV_Kretinsky.pdf","access_level":"open_access"}]},{"scopus_import":"1","day":"06","month":"02","article_processing_charge":"No","publication_identifier":{"eissn":["2642-9381"],"isbn":["9781665493475"]},"publication":"2023 IEEE/CVF Winter Conference on Applications of Computer Vision","citation":{"ama":"Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under distribution shift. In: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/wacv56688.2023.00278","ista":"Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision.","ieee":"S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training under distribution shift,” in 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Waikoloa, HI, United States, 2023.","apa":"Sinha, S., Gehler, P., Locatello, F., & Schiele, B. (2023). TeST: Test-time Self-Training under distribution shift. In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Waikoloa, HI, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/wacv56688.2023.00278","mla":"Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.” 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/wacv56688.2023.00278.","short":"S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023.","chicago":"Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele. “TeST: Test-Time Self-Training under Distribution Shift.” In 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/wacv56688.2023.00278."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.11459"}],"external_id":{"arxiv":["2209.11459"]},"quality_controlled":"1","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","end_date":"2023-01-07","location":"Waikoloa, HI, United States","start_date":"2023-01-02"},"date_published":"2023-02-06T00:00:00Z","doi":"10.1109/wacv56688.2023.00278","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks:\r\nobject detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. "}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14105","year":"2023","title":"TeST: Test-time Self-Training under distribution shift","publication_status":"published","status":"public","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"FrLo"}],"author":[{"first_name":"Samarth","last_name":"Sinha","full_name":"Sinha, Samarth"},{"last_name":"Gehler","first_name":"Peter","full_name":"Gehler, Peter"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Bernt","last_name":"Schiele","full_name":"Schiele, Bernt"}],"date_created":"2023-08-21T12:11:38Z","date_updated":"2023-09-06T10:26:56Z","oa_version":"Preprint"},{"acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","year":"2023","publication_status":"published","publisher":"EDP Sciences","department":[{"_id":"LiBu"}],"author":[{"last_name":"Mathis","first_name":"S.","full_name":"Mathis, S."},{"full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","last_name":"Bugnet","first_name":"Lisa Annabelle"}],"date_created":"2023-09-03T22:01:15Z","date_updated":"2023-09-06T11:05:58Z","volume":676,"article_number":"L9","file_date_updated":"2023-09-06T07:13:19Z","external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1051/0004-6361/202346832","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"_id":"14256","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["520"],"title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","status":"public","intvolume":" 676","file":[{"content_type":"application/pdf","file_size":458120,"creator":"dernst","access_level":"open_access","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","success":1,"date_updated":"2023-09-06T07:13:19Z","date_created":"2023-09-06T07:13:19Z","relation":"main_file","file_id":"14271"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.","lang":"eng"}],"publication":"Astronomy and Astrophysics","citation":{"short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.","chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 2023;676. doi:10.1051/0004-6361/202346832","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” Astronomy and Astrophysics, vol. 676. EDP Sciences, 2023.","apa":"Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9."},"article_type":"letter_note","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"quality_controlled":"1","isi":1,"doi":"10.1021/acs.jpclett.3c01707","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1948-7185"]},"year":"2023","acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","pmid":1,"publication_status":"published","department":[{"_id":"GradSch"}],"publisher":"American Chemical Society","author":[{"full_name":"Gamper, Jakob","last_name":"Gamper","first_name":"Jakob"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","last_name":"Kluibenschedl","full_name":"Kluibenschedl, Florian"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"first_name":"Thomas S.","last_name":"Hofer","full_name":"Hofer, Thomas S."}],"date_created":"2023-09-03T22:01:16Z","date_updated":"2023-09-06T11:04:31Z","volume":14,"file_date_updated":"2023-09-06T07:32:39Z","publication":"Journal of Physical Chemistry Letters","citation":{"ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403."},"article_type":"original","page":"7395-7403","date_published":"2023-08-11T00:00:00Z","scopus_import":"1","day":"11","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"14261","status":"public","ddc":["530","540"],"title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","intvolume":" 14","file":[{"file_name":"2023_JourPhysChemistry_Gamper.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4986859,"creator":"dernst","relation":"main_file","file_id":"14272","date_updated":"2023-09-06T07:32:39Z","date_created":"2023-09-06T07:32:39Z","checksum":"637454e2b3a357498d8d622d241c4bf6","success":1}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing.","lang":"eng"}],"issue":"33"},{"article_processing_charge":"No","day":"30","date_published":"2023-05-30T00:00:00Z","citation":{"ama":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. Benign overfitting in deep neural networks under lazy training. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:43105-43128.","ieee":"Z. Zhu, F. Liu, G. G. Chrysos, F. Locatello, and V. Cevher, “Benign overfitting in deep neural networks under lazy training,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, United States, 2023, vol. 202, pp. 43105–43128.","apa":"Zhu, Z., Liu, F., Chrysos, G. G., Locatello, F., & Cevher, V. (2023). Benign overfitting in deep neural networks under lazy training. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 43105–43128). Honolulu, Hawaii, United States: ML Research Press.","ista":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. 2023. Benign overfitting in deep neural networks under lazy training. Proceedings of the 40th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 202, 43105–43128.","short":"Z. Zhu, F. Liu, G.G. Chrysos, F. Locatello, V. Cevher, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 43105–43128.","mla":"Zhu, Zhenyu, et al. “Benign Overfitting in Deep Neural Networks under Lazy Training.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 43105–28.","chicago":"Zhu, Zhenyu, Fanghui Liu, Grigorios G Chrysos, Francesco Locatello, and Volkan Cevher. “Benign Overfitting in Deep Neural Networks under Lazy Training.” In Proceedings of the 40th International Conference on Machine Learning, 202:43105–28. ML Research Press, 2023."},"publication":"Proceedings of the 40th International Conference on Machine Learning","page":"43105-43128","abstract":[{"text":"This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory.","lang":"eng"}],"type":"conference","alternative_title":["PMLR"],"oa_version":"Preprint","_id":"14208","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 202","title":"Benign overfitting in deep neural networks under lazy training","status":"public","month":"05","conference":{"end_date":"2023-07-29","location":"Honolulu, Hawaii, United States","start_date":"2023-07-23","name":"International Conference on Machine Learning"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.19377"}],"external_id":{"arxiv":["2305.19377"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Zhu, Zhenyu","last_name":"Zhu","first_name":"Zhenyu"},{"full_name":"Liu, Fanghui","first_name":"Fanghui","last_name":"Liu"},{"first_name":"Grigorios G","last_name":"Chrysos","full_name":"Chrysos, Grigorios G"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Cevher, Volkan","first_name":"Volkan","last_name":"Cevher"}],"volume":202,"date_updated":"2023-09-13T08:46:46Z","date_created":"2023-08-22T14:18:18Z","year":"2023","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published"},{"abstract":[{"lang":"eng","text":"Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks."}],"extern":"1","article_number":"2304.10253","type":"preprint","author":[{"full_name":"Burg, Max F.","last_name":"Burg","first_name":"Max F."},{"first_name":"Florian","last_name":"Wenzel","full_name":"Wenzel, Florian"},{"full_name":"Zietlow, Dominik","last_name":"Zietlow","first_name":"Dominik"},{"full_name":"Horn, Max","last_name":"Horn","first_name":"Max"},{"full_name":"Makansi, Osama","last_name":"Makansi","first_name":"Osama"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"full_name":"Russell, Chris","last_name":"Russell","first_name":"Chris"}],"date_created":"2023-08-22T14:18:43Z","date_updated":"2023-09-13T08:51:56Z","oa_version":"Preprint","_id":"14209","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publication_status":"submitted","status":"public","title":"A data augmentation perspective on diffusion models and retrieval","department":[{"_id":"FrLo"}],"month":"04","day":"20","article_processing_charge":"No","doi":"10.48550/arXiv.2304.10253","date_published":"2023-04-20T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.10253","open_access":"1"}],"external_id":{"arxiv":["2304.10253"]},"citation":{"chicago":"Burg, Max F., Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco Locatello, and Chris Russell. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.10253.","mla":"Burg, Max F., et al. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” ArXiv, 2304.10253, doi:10.48550/arXiv.2304.10253.","short":"M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, ArXiv (n.d.).","ista":"Burg MF, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. A data augmentation perspective on diffusion models and retrieval. arXiv, 2304.10253.","ieee":"M. F. Burg et al., “A data augmentation perspective on diffusion models and retrieval,” arXiv. .","apa":"Burg, M. F., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., & Russell, C. (n.d.). A data augmentation perspective on diffusion models and retrieval. arXiv. https://doi.org/10.48550/arXiv.2304.10253","ama":"Burg MF, Wenzel F, Zietlow D, et al. A data augmentation perspective on diffusion models and retrieval. arXiv. doi:10.48550/arXiv.2304.10253"}},{"title":"Causal discovery with score matching on additive models with arbitrary noise","status":"public","publication_status":"published","department":[{"_id":"FrLo"}],"year":"2023","_id":"14211","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:19:21Z","date_updated":"2023-09-13T09:00:31Z","oa_version":"Preprint","author":[{"full_name":"Montagna, Francesco","last_name":"Montagna","first_name":"Francesco"},{"full_name":"Noceti, Nicoletta","first_name":"Nicoletta","last_name":"Noceti"},{"first_name":"Lorenzo","last_name":"Rosasco","full_name":"Rosasco, Lorenzo"},{"last_name":"Zhang","first_name":"Kun","full_name":"Zhang, Kun"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"type":"conference","extern":"1","abstract":[{"text":"Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data.","lang":"eng"}],"quality_controlled":"1","publication":"2nd Conference on Causal Learning and Reasoning","citation":{"mla":"Montagna, Francesco, et al. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” 2nd Conference on Causal Learning and Reasoning, 2023.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” In 2nd Conference on Causal Learning and Reasoning, 2023.","ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Causal discovery with score matching on additive models with arbitrary noise. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Causal discovery with score matching on additive models with arbitrary noise. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Causal discovery with score matching on additive models with arbitrary noise. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Causal discovery with score matching on additive models with arbitrary noise,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2304.03265"}],"external_id":{"arxiv":["2304.03265"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"CLeaR: Conference on Causal Learning and Reasoning","start_date":"2023-04-11","location":"Tübingen, Germany","end_date":"2023-04-14"},"date_published":"2023-04-01T00:00:00Z","scopus_import":"1","day":"01","month":"04","article_processing_charge":"No"},{"external_id":{"arxiv":["2304.03382"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2304.03382","open_access":"1"}],"citation":{"short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","mla":"Montagna, Francesco, et al. “Scalable Causal Discovery with Score Matching.” 2nd Conference on Causal Learning and Reasoning, 2023.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Scalable Causal Discovery with Score Matching.” In 2nd Conference on Causal Learning and Reasoning, 2023.","ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Scalable causal discovery with score matching. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Scalable causal discovery with score matching,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., & Locatello, F. (2023). Scalable causal discovery with score matching. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Scalable causal discovery with score matching. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning."},"publication":"2nd Conference on Causal Learning and Reasoning","quality_controlled":"1","date_published":"2023-04-01T00:00:00Z","conference":{"end_date":"2023-04-14","start_date":"2023-04-11","location":"Tübingen, Germany","name":"CLeaR: Conference on Causal Learning and Reasoning"},"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","month":"04","day":"01","_id":"14212","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"status":"public","title":"Scalable causal discovery with score matching","publication_status":"published","author":[{"full_name":"Montagna, Francesco","last_name":"Montagna","first_name":"Francesco"},{"full_name":"Noceti, Nicoletta","last_name":"Noceti","first_name":"Nicoletta"},{"last_name":"Rosasco","first_name":"Lorenzo","full_name":"Rosasco, Lorenzo"},{"first_name":"Kun","last_name":"Zhang","full_name":"Zhang, Kun"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"oa_version":"Preprint","date_created":"2023-08-22T14:19:40Z","date_updated":"2023-09-13T09:03:24Z","type":"conference","abstract":[{"lang":"eng","text":"This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar."}],"extern":"1"},{"day":"12","month":"04","article_processing_charge":"No","quality_controlled":"1","publication":"2nd Conference on Causal Learning and Reasoning","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.05169"}],"external_id":{"arxiv":["2301.05169"]},"oa":1,"citation":{"chicago":"Liu, Yuejiang, Alexandre Alahi, Chris Russell, Max Horn, Dominik Zietlow, Bernhard Schölkopf, and Francesco Locatello. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” In 2nd Conference on Causal Learning and Reasoning, 2023.","mla":"Liu, Yuejiang, et al. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” 2nd Conference on Causal Learning and Reasoning, 2023.","short":"Y. Liu, A. Alahi, C. Russell, M. Horn, D. Zietlow, B. Schölkopf, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","ista":"Liu Y, Alahi A, Russell C, Horn M, Zietlow D, Schölkopf B, Locatello F. 2023. Causal triplet: An open challenge for intervention-centric causal representation learning. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","ieee":"Y. Liu et al., “Causal triplet: An open challenge for intervention-centric causal representation learning,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","apa":"Liu, Y., Alahi, A., Russell, C., Horn, M., Zietlow, D., Schölkopf, B., & Locatello, F. (2023). Causal triplet: An open challenge for intervention-centric causal representation learning. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ama":"Liu Y, Alahi A, Russell C, et al. Causal triplet: An open challenge for intervention-centric causal representation learning. In: 2nd Conference on Causal Learning and Reasoning. ; 2023."},"language":[{"iso":"eng"}],"conference":{"name":"CLeaR: Conference on Causal Learning and Reasoning","start_date":"2023-04-11","location":"Tübingen, Germany","end_date":"2023-04-14"},"date_published":"2023-04-12T00:00:00Z","type":"conference","extern":"1","abstract":[{"lang":"eng","text":"Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work."}],"title":"Causal triplet: An open challenge for intervention-centric causal representation learning","status":"public","publication_status":"published","department":[{"_id":"FrLo"}],"_id":"14214","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","date_updated":"2023-09-13T09:23:08Z","date_created":"2023-08-22T14:20:18Z","oa_version":"Preprint","author":[{"full_name":"Liu, Yuejiang","first_name":"Yuejiang","last_name":"Liu"},{"full_name":"Alahi, Alexandre","first_name":"Alexandre","last_name":"Alahi"},{"full_name":"Russell, Chris","last_name":"Russell","first_name":"Chris"},{"full_name":"Horn, Max","first_name":"Max","last_name":"Horn"},{"first_name":"Dominik","last_name":"Zietlow","full_name":"Zietlow, Dominik"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}]},{"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2209.15430","open_access":"1"}],"citation":{"chicago":"Moschella, Luca, Valentino Maiorca, Marco Fumero, Antonio Norelli, Francesco Locatello, and Emanuele Rodolà. “Relative Representations Enable Zero-Shot Latent Space Communication.” In The 11th International Conference on Learning Representations, 2023.","short":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, E. Rodolà, in:, The 11th International Conference on Learning Representations, 2023.","mla":"Moschella, Luca, et al. “Relative Representations Enable Zero-Shot Latent Space Communication.” The 11th International Conference on Learning Representations, 2023.","ieee":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, and E. Rodolà, “Relative representations enable zero-shot latent space communication,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023.","apa":"Moschella, L., Maiorca, V., Fumero, M., Norelli, A., Locatello, F., & Rodolà, E. (2023). Relative representations enable zero-shot latent space communication. In The 11th International Conference on Learning Representations. Kigali, Rwanda.","ista":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. 2023. Relative representations enable zero-shot latent space communication. The 11th International Conference on Learning Representations. International Conference on Machine Learning Representations.","ama":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. Relative representations enable zero-shot latent space communication. In: The 11th International Conference on Learning Representations. ; 2023."},"oa":1,"external_id":{"arxiv":["2209.15430"]},"publication":"The 11th International Conference on Learning Representations","language":[{"iso":"eng"}],"date_published":"2023-05-01T00:00:00Z","conference":{"name":"International Conference on Machine Learning Representations","end_date":"2023-05-05","start_date":"2023-05-01","location":"Kigali, Rwanda"},"article_processing_charge":"No","month":"05","day":"01","department":[{"_id":"FrLo"}],"title":"Relative representations enable zero-shot latent space communication","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14217","year":"2023","oa_version":"Preprint","date_updated":"2023-09-13T09:44:26Z","date_created":"2023-08-22T14:22:20Z","author":[{"first_name":"Luca","last_name":"Moschella","full_name":"Moschella, Luca"},{"full_name":"Maiorca, Valentino","last_name":"Maiorca","first_name":"Valentino"},{"last_name":"Fumero","first_name":"Marco","full_name":"Fumero, Marco"},{"last_name":"Norelli","first_name":"Antonio","full_name":"Norelli, Antonio"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"last_name":"Rodolà","first_name":"Emanuele","full_name":"Rodolà, Emanuele"}],"type":"conference","extern":"1","abstract":[{"lang":"eng","text":"Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers)."}]},{"quality_controlled":"1","citation":{"ieee":"M. Tangemann et al., “Unsupervised object learning via common fate,” in 2nd Conference on Causal Learning and Reasoning, Tübingen, Germany, 2023.","apa":"Tangemann, M., Schneider, S., Kügelgen, J. von, Locatello, F., Gehler, P., Brox, T., … Schölkopf, B. (2023). Unsupervised object learning via common fate. In 2nd Conference on Causal Learning and Reasoning. Tübingen, Germany.","ista":"Tangemann M, Schneider S, Kügelgen J von, Locatello F, Gehler P, Brox T, Kümmerer M, Bethge M, Schölkopf B. 2023. Unsupervised object learning via common fate. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning, 2110.06562.","ama":"Tangemann M, Schneider S, Kügelgen J von, et al. Unsupervised object learning via common fate. In: 2nd Conference on Causal Learning and Reasoning. ; 2023.","chicago":"Tangemann, Matthias, Steffen Schneider, Julius von Kügelgen, Francesco Locatello, Peter Gehler, Thomas Brox, Matthias Kümmerer, Matthias Bethge, and Bernhard Schölkopf. “Unsupervised Object Learning via Common Fate.” In 2nd Conference on Causal Learning and Reasoning, 2023.","short":"M. Tangemann, S. Schneider, J. von Kügelgen, F. Locatello, P. Gehler, T. Brox, M. Kümmerer, M. Bethge, B. Schölkopf, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","mla":"Tangemann, Matthias, et al. “Unsupervised Object Learning via Common Fate.” 2nd Conference on Causal Learning and Reasoning, 2110.06562, 2023."},"main_file_link":[{"url":"https://arxiv.org/abs/2110.06562","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2110.06562"]},"publication":"2nd Conference on Causal Learning and Reasoning","language":[{"iso":"eng"}],"date_published":"2023-04-15T00:00:00Z","conference":{"name":"CLeaR: Conference on Causal Learning and Reasoning","location":"Tübingen, Germany","start_date":"2023-04-11","end_date":"2023-04-14"},"article_processing_charge":"No","month":"04","day":"15","department":[{"_id":"FrLo"}],"status":"public","publication_status":"published","title":"Unsupervised object learning via common fate","_id":"14222","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2023-09-13T11:31:14Z","date_created":"2023-08-22T14:23:54Z","author":[{"full_name":"Tangemann, Matthias","last_name":"Tangemann","first_name":"Matthias"},{"full_name":"Schneider, Steffen","last_name":"Schneider","first_name":"Steffen"},{"full_name":"Kügelgen, Julius von","first_name":"Julius von","last_name":"Kügelgen"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"first_name":"Peter","last_name":"Gehler","full_name":"Gehler, Peter"},{"last_name":"Brox","first_name":"Thomas","full_name":"Brox, Thomas"},{"full_name":"Kümmerer, Matthias","last_name":"Kümmerer","first_name":"Matthias"},{"full_name":"Bethge, Matthias","first_name":"Matthias","last_name":"Bethge"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"type":"conference","article_number":"2110.06562","extern":"1","abstract":[{"text":"Learning generative object models from unlabelled videos is a long standing problem and required for causal scene modeling. We decompose this problem into three easier subtasks, and provide candidate solutions for each of them. Inspired by the Common Fate Principle of Gestalt Psychology, we first extract (noisy) masks of moving objects via unsupervised motion segmentation. Second, generative models are trained on the masks of the background and the moving objects, respectively. Third, background and foreground models are combined in a conditional \"dead leaves\" scene model to sample novel scene configurations where occlusions and depth layering arise naturally. To evaluate the individual stages, we introduce the Fishbowl dataset positioned between complex real-world scenes and common object-centric benchmarks of simplistic objects. We show that our approach allows learning generative models that generalize beyond the occlusions present in the input videos, and represent scenes in a modular fashion that allows sampling plausible scenes outside the training distribution by permitting, for instance, object numbers or densities not observed in the training set.","lang":"eng"}]},{"language":[{"iso":"eng"}],"conference":{"name":"ICLR: International Conference on Learning Representations","location":"Kigali, Rwanda","start_date":"2023-05-01","end_date":"2023-05-05"},"date_published":"2023-05-10T00:00:00Z","quality_controlled":"1","publication":"The 11th International Conference on Learning Representations","external_id":{"arxiv":["2209.14860"]},"citation":{"short":"M. Seitzer, M. Horn, A. Zadaianchuk, D. Zietlow, T. Xiao, C.-J.S.-G. Carl-Johann Simon-Gabriel, T. He, Z. Zhang, B. Schölkopf, T. Brox, F. Locatello, in:, The 11th International Conference on Learning Representations, 2023.","mla":"Seitzer, Maximilian, et al. “Bridging the Gap to Real-World Object-Centric Learning.” The 11th International Conference on Learning Representations, 2023.","chicago":"Seitzer, Maximilian, Max Horn, Andrii Zadaianchuk, Dominik Zietlow, Tianjun Xiao, Carl-Johann Simon-Gabriel Carl-Johann Simon-Gabriel, Tong He, et al. “Bridging the Gap to Real-World Object-Centric Learning.” In The 11th International Conference on Learning Representations, 2023.","ama":"Seitzer M, Horn M, Zadaianchuk A, et al. Bridging the gap to real-world object-centric learning. In: The 11th International Conference on Learning Representations. ; 2023.","apa":"Seitzer, M., Horn, M., Zadaianchuk, A., Zietlow, D., Xiao, T., Carl-Johann Simon-Gabriel, C.-J. S.-G., … Locatello, F. (2023). Bridging the gap to real-world object-centric learning. In The 11th International Conference on Learning Representations. Kigali, Rwanda.","ieee":"M. Seitzer et al., “Bridging the gap to real-world object-centric learning,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023.","ista":"Seitzer M, Horn M, Zadaianchuk A, Zietlow D, Xiao T, Carl-Johann Simon-Gabriel C-JS-G, He T, Zhang Z, Schölkopf B, Brox T, Locatello F. 2023. Bridging the gap to real-world object-centric learning. The 11th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.14860"}],"month":"05","day":"10","article_processing_charge":"No","date_updated":"2023-09-13T11:37:03Z","date_created":"2023-08-22T14:22:41Z","oa_version":"Preprint","author":[{"full_name":"Seitzer, Maximilian","last_name":"Seitzer","first_name":"Maximilian"},{"first_name":"Max","last_name":"Horn","full_name":"Horn, Max"},{"first_name":"Andrii","last_name":"Zadaianchuk","full_name":"Zadaianchuk, Andrii"},{"first_name":"Dominik","last_name":"Zietlow","full_name":"Zietlow, Dominik"},{"full_name":"Xiao, Tianjun","last_name":"Xiao","first_name":"Tianjun"},{"full_name":"Carl-Johann Simon-Gabriel, Carl-Johann Simon-Gabriel","last_name":"Carl-Johann Simon-Gabriel","first_name":"Carl-Johann Simon-Gabriel"},{"full_name":"He, Tong","last_name":"He","first_name":"Tong"},{"full_name":"Zhang, Zheng","first_name":"Zheng","last_name":"Zhang"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"first_name":"Thomas","last_name":"Brox","full_name":"Brox, Thomas"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"}],"status":"public","title":"Bridging the gap to real-world object-centric learning","publication_status":"published","department":[{"_id":"FrLo"}],"_id":"14218","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","extern":"1","abstract":[{"text":"Humans naturally decompose their environment into entities at the appropriate level of abstraction to act in the world. Allowing machine learning algorithms to derive this decomposition in an unsupervised way has become an important line of research. However, current methods are restricted to simulated data or require additional information in the form of motion or depth in order to successfully discover objects. In this work, we overcome this limitation by showing that reconstructing features from models trained in a self-supervised manner is a sufficient training signal for object-centric representations to arise in a fully unsupervised way. Our approach, DINOSAUR, significantly out-performs existing image-based object-centric learning models on simulated data and is the first unsupervised object-centric model that scales to real-world datasets such as COCO and PASCAL VOC. DINOSAUR is conceptually simple and shows competitive performance compared to more involved pipelines from the computer vision literature.","lang":"eng"}],"type":"conference"},{"type":"conference","abstract":[{"text":"In this paper, we show that recent advances in self-supervised feature\r\nlearning enable unsupervised object discovery and semantic segmentation with a\r\nperformance that matches the state of the field on supervised semantic\r\nsegmentation 10 years ago. We propose a methodology based on unsupervised\r\nsaliency masks and self-supervised feature clustering to kickstart object\r\ndiscovery followed by training a semantic segmentation network on pseudo-labels\r\nto bootstrap the system on images with multiple objects. We present results on\r\nPASCAL VOC that go far beyond the current state of the art (50.0 mIoU), and we\r\nreport for the first time results on MS COCO for the whole set of 81 classes:\r\nour method discovers 34 categories with more than $20\\%$ IoU, while obtaining\r\nan average IoU of 19.6 for all 81 categories.","lang":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14219","year":"2023","title":"Unsupervised semantic segmentation with self-supervised object-centric representations","publication_status":"published","status":"public","department":[{"_id":"FrLo"}],"author":[{"first_name":"Andrii","last_name":"Zadaianchuk","full_name":"Zadaianchuk, Andrii"},{"first_name":"Matthaeus","last_name":"Kleindessner","full_name":"Kleindessner, Matthaeus"},{"full_name":"Zhu, Yi","first_name":"Yi","last_name":"Zhu"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"full_name":"Brox, Thomas","last_name":"Brox","first_name":"Thomas"}],"date_updated":"2023-09-13T11:25:43Z","date_created":"2023-08-22T14:22:58Z","oa_version":"Preprint","day":"01","month":"05","article_processing_charge":"No","publication":"The 11th International Conference on Learning Representations","external_id":{"arxiv":["2207.05027"]},"citation":{"chicago":"Zadaianchuk, Andrii, Matthaeus Kleindessner, Yi Zhu, Francesco Locatello, and Thomas Brox. “Unsupervised Semantic Segmentation with Self-Supervised Object-Centric Representations.” In The 11th International Conference on Learning Representations, 2023.","short":"A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, T. Brox, in:, The 11th International Conference on Learning Representations, 2023.","mla":"Zadaianchuk, Andrii, et al. “Unsupervised Semantic Segmentation with Self-Supervised Object-Centric Representations.” The 11th International Conference on Learning Representations, 2023.","apa":"Zadaianchuk, A., Kleindessner, M., Zhu, Y., Locatello, F., & Brox, T. (2023). Unsupervised semantic segmentation with self-supervised object-centric representations. In The 11th International Conference on Learning Representations. Kigali, Rwanda.","ieee":"A. Zadaianchuk, M. Kleindessner, Y. Zhu, F. Locatello, and T. Brox, “Unsupervised semantic segmentation with self-supervised object-centric representations,” in The 11th International Conference on Learning Representations, Kigali, Rwanda, 2023.","ista":"Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. 2023. Unsupervised semantic segmentation with self-supervised object-centric representations. The 11th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Zadaianchuk A, Kleindessner M, Zhu Y, Locatello F, Brox T. Unsupervised semantic segmentation with self-supervised object-centric representations. In: The 11th International Conference on Learning Representations. ; 2023."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2207.05027","open_access":"1"}],"quality_controlled":"1","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Kigali, Rwanda","start_date":"2023-05-01","end_date":"2023-05-05"},"date_published":"2023-05-01T00:00:00Z","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"date_published":"2023-07-18T00:00:00Z","doi":"10.48550/arXiv.2307.09552","external_id":{"arxiv":["2307.09552"]},"citation":{"chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09552.","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” ArXiv, 2307.09552, doi:10.48550/arXiv.2307.09552.","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.).","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., & Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. arXiv. https://doi.org/10.48550/arXiv.2307.09552","ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” arXiv. .","ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv. doi:10.48550/arXiv.2307.09552"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.09552","open_access":"1"}],"oa":1,"publication":"arXiv","article_processing_charge":"No","day":"18","month":"07","oa_version":"Preprint","date_updated":"2023-09-13T12:47:53Z","date_created":"2023-09-13T12:44:59Z","author":[{"full_name":"Faller, Philipp M.","first_name":"Philipp M.","last_name":"Faller"},{"full_name":"Vankadara, Leena Chennuru","last_name":"Vankadara","first_name":"Leena Chennuru"},{"full_name":"Mastakouri, Atalanti A.","first_name":"Atalanti A.","last_name":"Mastakouri"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Janzing, Dominik","last_name":"Janzing","first_name":"Dominik"}],"department":[{"_id":"FrLo"}],"status":"public","title":"Self-compatibility: Evaluating causal discovery without ground truth","publication_status":"submitted","year":"2023","_id":"14333","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection."}],"type":"preprint","article_number":"2307.09552"},{"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"EdHa"}],"acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","year":"2023","date_created":"2023-09-06T08:30:59Z","date_updated":"2023-09-15T06:39:17Z","volume":1,"author":[{"last_name":"Boocock","first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","full_name":"Boocock, Daniel R"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"article_number":"013001","file_date_updated":"2023-09-15T06:30:50Z","ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/prxlife.1.013001","month":"07","publication_identifier":{"issn":["2835-8279"]},"status":"public","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","ddc":["570"],"intvolume":" 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14277","file":[{"relation":"main_file","file_id":"14335","date_created":"2023-09-15T06:30:50Z","date_updated":"2023-09-15T06:30:50Z","checksum":"f881d98c89eb9f1aa136d7b781511553","success":1,"file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2559520,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.","lang":"eng"}],"issue":"1","article_type":"original","publication":"PRX Life","citation":{"ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001."},"date_published":"2023-07-20T00:00:00Z","day":"20","article_processing_charge":"Yes","has_accepted_license":"1"},{"department":[{"_id":"JoCs"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","volume":42,"date_created":"2023-09-10T22:01:11Z","date_updated":"2023-09-15T07:14:12Z","author":[{"full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570"},{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola"},{"last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"article_number":"113015","ec_funded":1,"file_date_updated":"2023-09-15T07:12:46Z","project":[{"grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37632747"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2023.113015","publication_identifier":{"eissn":["2211-1247"]},"month":"09","intvolume":" 42","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","status":"public","ddc":["570"],"_id":"14314","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":4879455,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_CellPress_Nardin.pdf","checksum":"ca77a304fb813c292550b8604b0fb41d","success":1,"date_updated":"2023-09-15T07:12:46Z","date_created":"2023-09-15T07:12:46Z","relation":"main_file","file_id":"14337"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"article_type":"original","citation":{"chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier, 2023, doi:10.1016/j.celrep.2023.113015.","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” Cell Reports, vol. 42, no. 9. Elsevier, 2023.","apa":"Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015","ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 2023;42(9). doi:10.1016/j.celrep.2023.113015"},"publication":"Cell Reports","date_published":"2023-09-26T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"26"},{"author":[{"full_name":"Cho, Ukrae H.","last_name":"Cho","first_name":"Ukrae H."},{"first_name":"Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W"}],"date_updated":"2023-09-15T07:07:10Z","date_created":"2023-09-10T22:01:11Z","volume":12,"acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"MaHe"}],"publisher":"eLife Sciences Publications","file_date_updated":"2023-09-15T06:59:10Z","article_number":"RP89066","doi":"10.7554/eLife.89066","language":[{"iso":"eng"}],"external_id":{"pmid":["37665327"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["2050-084X"]},"oa_version":"Published Version","file":[{"file_id":"14336","relation":"main_file","success":1,"checksum":"db24bf3d595507387b48d3799c33e289","date_created":"2023-09-15T06:59:10Z","date_updated":"2023-09-15T06:59:10Z","access_level":"open_access","file_name":"2023_eLife_Cho.pdf","creator":"dernst","content_type":"application/pdf","file_size":3703097}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14315","status":"public","ddc":["570"],"title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","intvolume":" 12","abstract":[{"text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-04T00:00:00Z","publication":"eLife","citation":{"ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12. eLife Sciences Publications, 2023.","apa":"Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.89066","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023)."},"article_type":"original","day":"04","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1"},{"scopus_import":"1","day":"28","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Electronic Journal of Combinatorics","citation":{"ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 2023;30(3). doi:10.37236/11714","apa":"Anastos, M., Fabian, D., Müyesser, A., & Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11714","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” Electronic Journal of Combinatorics, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:10.37236/11714.","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11714."},"article_type":"original","date_published":"2023-07-28T00:00:00Z","type":"journal_article","abstract":[{"text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities.","lang":"eng"}],"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14319","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","ddc":["510"],"status":"public","intvolume":" 30","oa_version":"Published Version","file":[{"creator":"dernst","file_size":247917,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_elecJournCombinatorics_Anastos.pdf","success":1,"checksum":"52c46c8cb329f9aaee9ade01525f317b","date_updated":"2023-09-15T08:02:09Z","date_created":"2023-09-15T08:02:09Z","file_id":"14338","relation":"main_file"}],"month":"07","publication_identifier":{"eissn":["1077-8926"]},"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["2212.03100"]},"oa":1,"quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"doi":"10.37236/11714","language":[{"iso":"eng"}],"article_number":"P3.10","file_date_updated":"2023-09-15T08:02:09Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","year":"2023","acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","publication_status":"published","publisher":"Electronic Journal of Combinatorics","department":[{"_id":"MaKw"}],"author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"},{"full_name":"Fabian, David","first_name":"David","last_name":"Fabian"},{"last_name":"Müyesser","first_name":"Alp","full_name":"Müyesser, Alp"},{"last_name":"Szabó","first_name":"Tibor","full_name":"Szabó, Tibor"}],"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-15T08:12:30Z","volume":30},{"date_published":"2023-07-17T00:00:00Z","page":"16-39","publication":"Computer Aided Verification","citation":{"mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:10.1007/978-3-031-37709-9_2.","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: Computer Aided Verification. Vol 13966. Springer Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","apa":"Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In Computer Aided Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 16–39."},"day":"17","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_LNCS_Sun.pdf","creator":"dernst","file_size":624647,"content_type":"application/pdf","file_id":"14348","relation":"main_file","success":1,"checksum":"42917e086f8c7699f3bccf84f74fe000","date_created":"2023-09-20T08:24:47Z","date_updated":"2023-09-20T08:24:47Z"}],"ddc":["000"],"title":"Automated tail bound analysis for probabilistic recurrence relations","status":"public","intvolume":" 13966","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14318","abstract":[{"text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22"},"doi":"10.1007/978-3-031-37709-9_2","quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"07","publication_identifier":{"isbn":["9783031377082"],"eissn":["1611-3349"],"issn":["0302-9743"]},"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T08:25:57Z","volume":13966,"author":[{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"related_material":{"link":[{"url":"https://github.com/boyvolcano/PRR","relation":"software"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","year":"2023","file_date_updated":"2023-09-20T08:24:47Z","ec_funded":1},{"publication":"International Conference on Computer Aided Verification","citation":{"ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 86–112.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In International Conference on Computer Aided Verification (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: International Conference on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In International Conference on Computer Aided Verification, 13966:86–112. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” International Conference on Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112."},"page":"86-112","date_published":"2023-07-17T00:00:00Z","scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","_id":"14317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","ddc":["000"],"status":"public","intvolume":" 13966","oa_version":"Published Version","file":[{"creator":"dernst","file_size":531745,"content_type":"application/pdf","file_name":"2023_LNCS_Akshay.pdf","access_level":"open_access","date_created":"2023-09-20T08:46:43Z","date_updated":"2023-09-20T08:46:43Z","success":1,"checksum":"f143c8eedf609f20f2aad2eeb496d53f","file_id":"14349","relation":"main_file"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"conference":{"name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22"},"doi":"10.1007/978-3-031-37709-9_5","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["9783031377082"],"eissn":["1611-3349"],"issn":["0302-9743"]},"acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","year":"2023","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","author":[{"first_name":"S.","last_name":"Akshay","full_name":"Akshay, S."},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"date_updated":"2023-09-20T09:04:40Z","date_created":"2023-09-10T22:01:12Z","volume":13966,"file_date_updated":"2023-09-20T08:46:43Z","ec_funded":1},{"year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"The Company of Biologists","author":[{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"last_name":"Shimamura","first_name":"Hiroki","full_name":"Shimamura, Hiroki"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"last_name":"Toshima","first_name":"Junko Y.","full_name":"Toshima, Junko Y."},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"date_created":"2023-09-10T22:01:12Z","date_updated":"2023-09-20T09:14:15Z","volume":136,"article_number":"jcs261448","external_id":{"pmid":["37539494"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"quality_controlled":"1","doi":"10.1242/jcs.261448","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"_id":"14316","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","status":"public","intvolume":" 136","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway."}],"issue":"17","publication":"Journal of Cell Science","citation":{"short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., & Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261448","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol. 136, no. 17. The Company of Biologists, 2023.","ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448."},"article_type":"original","date_published":"2023-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"date_published":"2023-09-15T00:00:00Z","publication":"Physical Review B","citation":{"ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 2023;108(12). doi:10.1103/physrevb.108.125411","ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., & Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.125411","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” Physical Review B, vol. 108, no. 12. American Physical Society, 2023.","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:10.1103/physrevb.108.125411.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.125411."},"article_type":"original","day":"15","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"14320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","intvolume":" 108","abstract":[{"lang":"eng","text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance."}],"issue":"12","type":"journal_article","doi":"10.1103/physrevb.108.125411","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2210.06310"}],"external_id":{"arxiv":["2210.06310"]},"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"author":[{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M"},{"first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"full_name":"Zibrov, Alexander A.","last_name":"Zibrov","first_name":"Alexander A."},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"date_updated":"2023-09-20T09:38:24Z","date_created":"2023-09-12T07:12:12Z","volume":108,"year":"2023","acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"article_number":"125411"},{"file":[{"file_id":"12753","relation":"source_file","checksum":"5d2de651ef9449c1b8dc27148ca74777","date_created":"2023-03-23T16:42:56Z","date_updated":"2023-03-23T16:42:56Z","access_level":"closed","file_name":"Thesis_sub_PBrighi.zip","creator":"pbrighi","file_size":42167561,"content_type":"application/zip"},{"date_updated":"2023-03-23T16:43:14Z","date_created":"2023-03-23T16:43:14Z","checksum":"7caa153d4a5b0873a79358787d2dfe1e","success":1,"relation":"main_file","file_id":"12754","file_size":13977000,"content_type":"application/pdf","creator":"pbrighi","file_name":"Thesis_PBrighi.pdf","access_level":"open_access"}],"oa_version":"None","status":"public","ddc":["530"],"title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12732","abstract":[{"lang":"eng","text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-03-21T00:00:00Z","page":"158","citation":{"ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732."},"day":"21","article_processing_charge":"No","has_accepted_license":"1","date_created":"2023-03-17T13:30:48Z","date_updated":"2023-09-20T10:44:12Z","author":[{"full_name":"Brighi, Pietro","first_name":"Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11470"},{"id":"8308","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"11469"},{"id":"12750","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"year":"2023","file_date_updated":"2023-03-23T16:43:14Z","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12732","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"month":"03","publication_identifier":{"issn":["2663-337X"]}},{"volume":15,"date_created":"2023-09-14T13:08:23Z","date_updated":"2023-09-20T10:46:29Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12750"}]},"author":[{"full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","first_name":"Pietro"},{"first_name":"Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"department":[{"_id":"MaSe"}],"publisher":"SciPost Foundation","publication_status":"published","year":"2023","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","ec_funded":1,"file_date_updated":"2023-09-20T10:46:10Z","article_number":"093","language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.15.3.093","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2210.15607"]},"oa":1,"publication_identifier":{"issn":["2542-4653"]},"month":"09","oa_version":"Published Version","file":[{"checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","success":1,"date_created":"2023-09-20T10:46:10Z","date_updated":"2023-09-20T10:46:10Z","relation":"main_file","file_id":"14350","content_type":"application/pdf","file_size":4866506,"creator":"dernst","access_level":"open_access","file_name":"2023_SciPostPhysics_Brighi.pdf"}],"intvolume":" 15","ddc":["530"],"status":"public","title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","_id":"14334","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-13T00:00:00Z","article_type":"original","citation":{"chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.3.093.","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” SciPost Physics, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.3.093.","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” SciPost Physics, vol. 15, no. 3. SciPost Foundation, 2023.","apa":"Brighi, P., Ljubotina, M., & Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.3.093","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.","ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 2023;15(3). doi:10.21468/scipostphys.15.3.093"},"publication":"SciPost Physics","article_processing_charge":"No","has_accepted_license":"1","day":"13","keyword":["General Physics and Astronomy"]},{"month":"09","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37694742"],"arxiv":["2306.17592"]},"quality_controlled":"1","project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338","grant_number":"101062862"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"doi":"10.1063/5.0165806","language":[{"iso":"eng"}],"article_number":"104103","file_date_updated":"2023-09-13T09:34:20Z","ec_funded":1,"year":"2023","acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","pmid":1,"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"MiLe"}],"author":[{"full_name":"Al Hyder, Ragheed","last_name":"Al Hyder","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e"},{"last_name":"Cappellaro","first_name":"Alberto","orcid":"0000-0001-6110-2359","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","full_name":"Cappellaro, Alberto"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"date_updated":"2023-09-20T09:48:12Z","date_created":"2023-09-13T09:25:09Z","volume":159,"scopus_import":"1","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"day":"11","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"The Journal of Chemical Physics","citation":{"chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0165806.","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” The Journal of Chemical Physics, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:10.1063/5.0165806.","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023).","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” The Journal of Chemical Physics, vol. 159, no. 10. AIP Publishing, 2023.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0165806","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 2023;159(10). doi:10.1063/5.0165806"},"article_type":"original","date_published":"2023-09-11T00:00:00Z","type":"journal_article","abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14321","status":"public","title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","ddc":["530"],"intvolume":" 159","file":[{"file_size":5749653,"content_type":"application/pdf","creator":"acappell","access_level":"open_access","file_name":"104103_1_5.0165806.pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","success":1,"date_updated":"2023-09-13T09:34:20Z","date_created":"2023-09-13T09:34:20Z","relation":"main_file","file_id":"14322"}],"oa_version":"Published Version"},{"scopus_import":"1","day":"28","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"Applied Physics Letters","citation":{"ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 2023;123(9). doi:10.1063/5.0161713","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” Applied Physics Letters, vol. 123, no. 9. AIP Publishing, 2023.","apa":"Lorenc, D., & Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0161713","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.","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:10.1063/5.0161713.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” Applied Physics Letters. AIP Publishing, 2023. https://doi.org/10.1063/5.0161713."},"article_type":"original","date_published":"2023-08-28T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14342","title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","ddc":["530"],"status":"public","intvolume":" 123","file":[{"content_type":"application/pdf","file_size":1486715,"creator":"dernst","file_name":"2023_ApplPhysLetter_Lorenc.pdf","access_level":"open_access","date_created":"2023-09-20T11:36:16Z","date_updated":"2023-09-20T11:36:16Z","checksum":"89a1b604d58b209fec66c6b6f919ac98","success":1,"relation":"main_file","file_id":"14353"}],"oa_version":"Published Version","month":"08","publication_identifier":{"issn":["0003-6951"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2306.09043"]},"quality_controlled":"1","doi":"10.1063/5.0161713","language":[{"iso":"eng"}],"article_number":"091104","file_date_updated":"2023-09-20T11:36:16Z","year":"2023","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","publication_status":"published","department":[{"_id":"ZhAl"}],"publisher":"AIP Publishing","author":[{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-09-17T22:01:09Z","date_updated":"2023-09-20T11:50:06Z","volume":123},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"09","external_id":{"pmid":["37673988"]},"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","doi":"10.1038/s41586-023-06399-5","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"pmid":1,"year":"2023","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.","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","relation":"press_release","description":"News on ISTA website"}]},"author":[{"full_name":"Scarselli, Davide","first_name":"Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271"},{"first_name":"Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}],"volume":621,"date_updated":"2023-09-20T12:10:22Z","date_created":"2023-09-17T22:01:09Z","scopus_import":"1","article_processing_charge":"No","day":"07","citation":{"chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06399-5.","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” Nature, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:10.1038/s41586-023-06399-5.","ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” Nature, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., & Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06399-5","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.","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 2023;621(7977):71-74. doi:10.1038/s41586-023-06399-5"},"publication":"Nature","page":"71-74","article_type":"original","date_published":"2023-09-07T00:00:00Z","type":"journal_article","issue":"7977","abstract":[{"lang":"eng","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."}],"_id":"14341","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 621","title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","status":"public","oa_version":"None"},{"date_updated":"2023-09-25T08:50:10Z","date_created":"2023-09-25T08:44:29Z","volume":25,"author":[{"last_name":"Accogli","first_name":"Andrea","full_name":"Accogli, Andrea"},{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"full_name":"Severino, Mariasavina","last_name":"Severino","first_name":"Mariasavina"},{"last_name":"Kim","first_name":"Sung-Hoon","full_name":"Kim, Sung-Hoon"},{"full_name":"Huang, Kevin","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang","first_name":"Kevin"},{"first_name":"Clarissa","last_name":"Rocca","full_name":"Rocca, Clarissa"},{"full_name":"Landsverk, Megan","last_name":"Landsverk","first_name":"Megan"},{"first_name":"Maha S.","last_name":"Zaki","full_name":"Zaki, Maha S."},{"full_name":"Al-Maawali, Almundher","last_name":"Al-Maawali","first_name":"Almundher"},{"last_name":"Srinivasan","first_name":"Varunvenkat M.","full_name":"Srinivasan, Varunvenkat M."},{"full_name":"Al-Thihli, Khalid","first_name":"Khalid","last_name":"Al-Thihli"},{"full_name":"Schaefer, G. Bradly","first_name":"G. Bradly","last_name":"Schaefer"},{"last_name":"Davis","first_name":"Monica","full_name":"Davis, Monica"},{"first_name":"Davide","last_name":"Tonduti","full_name":"Tonduti, Davide"},{"last_name":"Doneda","first_name":"Chiara","full_name":"Doneda, Chiara"},{"last_name":"Marten","first_name":"Lara M.","full_name":"Marten, Lara M."},{"full_name":"Mühlhausen, Chris","last_name":"Mühlhausen","first_name":"Chris"},{"last_name":"Gomez","first_name":"Maria","full_name":"Gomez, Maria"},{"full_name":"Lamantea, Eleonora","first_name":"Eleonora","last_name":"Lamantea"},{"first_name":"Rafael","last_name":"Mena","full_name":"Mena, Rafael"},{"first_name":"Mathilde","last_name":"Nizon","full_name":"Nizon, Mathilde"},{"full_name":"Procaccio, Vincent","first_name":"Vincent","last_name":"Procaccio"},{"first_name":"Amber","last_name":"Begtrup","full_name":"Begtrup, Amber"},{"full_name":"Telegrafi, Aida","first_name":"Aida","last_name":"Telegrafi"},{"full_name":"Cui, Hong","last_name":"Cui","first_name":"Hong"},{"full_name":"Schulz, Heidi L.","last_name":"Schulz","first_name":"Heidi L."},{"full_name":"Mohr, Julia","last_name":"Mohr","first_name":"Julia"},{"last_name":"Biskup","first_name":"Saskia","full_name":"Biskup, Saskia"},{"full_name":"Loos, Mariana Amina","first_name":"Mariana Amina","last_name":"Loos"},{"full_name":"Aráoz, Hilda Verónica","last_name":"Aráoz","first_name":"Hilda Verónica"},{"last_name":"Salpietro","first_name":"Vincenzo","full_name":"Salpietro, Vincenzo"},{"full_name":"Keppen, Laura Davis","last_name":"Keppen","first_name":"Laura Davis"},{"full_name":"Chitre, Manali","first_name":"Manali","last_name":"Chitre"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"full_name":"Raymond, Lucy","last_name":"Raymond","first_name":"Lucy"},{"first_name":"Julie","last_name":"Vogt","full_name":"Vogt, Julie"},{"first_name":"Lindsey B.","last_name":"Sawyer","full_name":"Sawyer, Lindsey B."},{"last_name":"Basinger","first_name":"Alice A.","full_name":"Basinger, Alice A."},{"first_name":"Signe Vandal","last_name":"Pedersen","full_name":"Pedersen, Signe Vandal"},{"full_name":"Pearson, Toni S.","first_name":"Toni S.","last_name":"Pearson"},{"full_name":"Grange, Dorothy K.","last_name":"Grange","first_name":"Dorothy K."},{"full_name":"Lingappa, Lokesh","first_name":"Lokesh","last_name":"Lingappa"},{"full_name":"McDunnah, Paige","last_name":"McDunnah","first_name":"Paige"},{"first_name":"Rita","last_name":"Horvath","full_name":"Horvath, Rita"},{"first_name":"Benjamin","last_name":"Cognè","full_name":"Cognè, Benjamin"},{"full_name":"Isidor, Bertrand","first_name":"Bertrand","last_name":"Isidor"},{"full_name":"Hahn, Andreas","last_name":"Hahn","first_name":"Andreas"},{"full_name":"Gripp, Karen W.","first_name":"Karen W.","last_name":"Gripp"},{"first_name":"Seyed Mehdi","last_name":"Jafarnejad","full_name":"Jafarnejad, Seyed Mehdi"},{"full_name":"Østergaard, Elsebet","first_name":"Elsebet","last_name":"Østergaard"},{"full_name":"Prada, Carlos E.","last_name":"Prada","first_name":"Carlos E."},{"full_name":"Ghezzi, Daniele","first_name":"Daniele","last_name":"Ghezzi"},{"first_name":"Vykuntaraju K.","last_name":"Gowda","full_name":"Gowda, Vykuntaraju K."},{"full_name":"Taylor, Robert W.","first_name":"Robert W.","last_name":"Taylor"},{"last_name":"Sonenberg","first_name":"Nahum","full_name":"Sonenberg, Nahum"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"full_name":"Sissler, Marie","first_name":"Marie","last_name":"Sissler"},{"last_name":"Varshney","first_name":"Gaurav K.","full_name":"Varshney, Gaurav K."},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"}],"publication_status":"published","publisher":"Elsevier","year":"2023","extern":"1","file_date_updated":"2023-09-25T08:48:54Z","article_number":"100938","language":[{"iso":"eng"}],"doi":"10.1016/j.gim.2023.100938","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11","publication_identifier":{"issn":["1098-3600"]},"oa_version":"Published Version","file":[{"file_name":"2023_GeneticsMedicine_Accogli.pdf","access_level":"open_access","creator":"dernst","file_size":4105513,"content_type":"application/pdf","file_id":"14369","relation":"main_file","date_created":"2023-09-25T08:48:54Z","date_updated":"2023-09-25T08:48:54Z","success":1,"checksum":"440f0cd8a2ffcbe03c015c1746728387"}],"status":"public","title":"Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder","ddc":["570"],"intvolume":" 25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14368","abstract":[{"lang":"eng","text":"Purpose: \r\nBiallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants.\r\nMethods:\r\nExome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model.\r\nResults:\r\nWe report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model.\r\nConclusion:\r\nWe define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity."}],"issue":"11","type":"journal_article","date_published":"2023-11-01T00:00:00Z","article_type":"original","publication":"Genetics in Medicine","citation":{"apa":"Accogli, A., Lin, S.-J., Severino, M., Kim, S.-H., Huang, K., Rocca, C., … Maroofian, R. (2023). Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2023.100938","ieee":"A. Accogli et al., “Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder,” Genetics in Medicine, vol. 25, no. 11. Elsevier, 2023.","ista":"Accogli A, Lin S-J, Severino M, Kim S-H, Huang K, Rocca C, Landsverk M, Zaki MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. 2023. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in Medicine. 25(11), 100938.","ama":"Accogli A, Lin S-J, Severino M, et al. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in Medicine. 2023;25(11). doi:10.1016/j.gim.2023.100938","chicago":"Accogli, Andrea, Sheng-Jia Lin, Mariasavina Severino, Sung-Hoon Kim, Kevin Huang, Clarissa Rocca, Megan Landsverk, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” Genetics in Medicine. Elsevier, 2023. https://doi.org/10.1016/j.gim.2023.100938.","short":"A. Accogli, S.-J. Lin, M. Severino, S.-H. Kim, K. Huang, C. Rocca, M. Landsverk, M.S. Zaki, A. Al-Maawali, V.M. Srinivasan, K. Al-Thihli, G.B. Schaefer, M. Davis, D. Tonduti, C. Doneda, L.M. Marten, C. Mühlhausen, M. Gomez, E. Lamantea, R. Mena, M. Nizon, V. Procaccio, A. Begtrup, A. Telegrafi, H. Cui, H.L. Schulz, J. Mohr, S. Biskup, M.A. Loos, H.V. Aráoz, V. Salpietro, L.D. Keppen, M. Chitre, C. Petree, L. Raymond, J. Vogt, L.B. Sawyer, A.A. Basinger, S.V. Pedersen, T.S. Pearson, D.K. Grange, L. Lingappa, P. McDunnah, R. Horvath, B. Cognè, B. Isidor, A. Hahn, K.W. Gripp, S.M. Jafarnejad, E. Østergaard, C.E. Prada, D. Ghezzi, V.K. Gowda, R.W. Taylor, N. Sonenberg, H. Houlden, M. Sissler, G.K. Varshney, R. Maroofian, Genetics in Medicine 25 (2023).","mla":"Accogli, Andrea, et al. “Clinical, Neuroradiological, and Molecular Characterization of Mitochondrial Threonyl-TRNA-Synthetase (TARS2)-Related Disorder.” Genetics in Medicine, vol. 25, no. 11, 100938, Elsevier, 2023, doi:10.1016/j.gim.2023.100938."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["Genetics (clinical)"],"scopus_import":"1"},{"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2302.06420"]},"oa":1,"quality_controlled":"1","doi":"10.4230/LIPIcs.ITP.2023.15","conference":{"name":"ITP: International Conference on Interactive Theorem Proving","end_date":"2023-08-04","start_date":"2023-07-31","location":"Bialystok, Poland"},"language":[{"iso":"eng"}],"article_number":"15","file_date_updated":"2023-08-07T11:55:43Z","year":"2023","acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/grammars/tree/publish"}]},"author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","first_name":"Martin","last_name":"Dvorak","full_name":"Dvorak, Martin"},{"last_name":"Blanchette","first_name":"Jasmin","full_name":"Blanchette, Jasmin"}],"volume":268,"date_updated":"2023-09-25T11:04:29Z","date_created":"2023-06-05T07:29:05Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","citation":{"chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15.","mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.","apa":"Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15"},"publication":"14th International Conference on Interactive Theorem Proving","date_published":"2023-07-27T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13120","intvolume":" 268","status":"public","ddc":["000"],"title":"Closure properties of general grammars - formally verified","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":715976,"file_name":"2023_LIPIcS_Dvorak.pdf","access_level":"open_access","date_updated":"2023-08-07T11:55:43Z","date_created":"2023-08-07T11:55:43Z","success":1,"checksum":"773a0197f05b67feaa6cb1e17ec3642d","file_id":"13982","relation":"main_file"}]},{"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-07-01T00:00:00Z","publication":"Journal of Graph Algorithms and Applications","citation":{"ista":"Arroyo Guevara AM, Felsner S. 2023. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 27(6), 433–457.","ieee":"A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing number,” Journal of Graph Algorithms and Applications, vol. 27, no. 6. Brown University, pp. 433–457, 2023.","apa":"Arroyo Guevara, A. M., & Felsner, S. (2023). Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00629","ama":"Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. Journal of Graph Algorithms and Applications. 2023;27(6):433-457. doi:10.7155/jgaa.00629","chicago":"Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications. Brown University, 2023. https://doi.org/10.7155/jgaa.00629.","mla":"Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing Number.” Journal of Graph Algorithms and Applications, vol. 27, no. 6, Brown University, 2023, pp. 433–57, doi:10.7155/jgaa.00629.","short":"A.M. Arroyo Guevara, S. Felsner, Journal of Graph Algorithms and Applications 27 (2023) 433–457."},"article_type":"original","page":"433-457","abstract":[{"lang":"eng","text":"Bundling crossings is a strategy which can enhance the readability\r\nof graph drawings. In this paper we consider good drawings, i.e., we require that\r\nany two edges have at most one common point which can be a common vertex or a\r\ncrossing. Our main result is that there is a polynomial-time algorithm to compute an\r\n8-approximation of the bundled crossing number of a good drawing with no toothed\r\nhole. In general the number of toothed holes has to be added to the 8-approximation.\r\nIn the special case of circular drawings the approximation factor is 8, this improves\r\nupon the 10-approximation of Fink et al. [14]. Our approach also works with the same\r\napproximation factor for families of pseudosegments, i.e., curves intersecting at most\r\nonce. We also show how to compute a 9/2-approximation when the intersection graph of\r\nthe pseudosegments is bipartite and has no toothed hole."}],"issue":"6","type":"journal_article","file":[{"file_name":"2023_JourGraphAlgorithms_Arroyo.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":865774,"file_id":"13979","relation":"main_file","date_created":"2023-08-07T08:00:48Z","date_updated":"2023-08-07T08:00:48Z","success":1,"checksum":"9c30d2b8e324cc1c904f2aeec92013a3"}],"oa_version":"Published Version","_id":"13969","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"title":"Approximating the bundled crossing number","status":"public","intvolume":" 27","month":"07","publication_identifier":{"issn":["1526-1719"]},"doi":"10.7155/jgaa.00629","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2109.14892"]},"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-08-07T08:00:48Z","ec_funded":1,"author":[{"full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara","first_name":"Alan M"},{"full_name":"Felsner, Stefan","last_name":"Felsner","first_name":"Stefan"}],"related_material":{"record":[{"id":"11185","relation":"earlier_version","status":"public"}]},"date_updated":"2023-09-25T10:56:10Z","date_created":"2023-08-06T22:01:11Z","volume":27,"acknowledgement":"This work was initiated during the Workshop on Geometric Graphs in November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during the workshop. The first author has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No 754411. The second author has been supported by the German Research Foundation DFG Project FE 340/12-1. An extended abstract of this paper has been published in the proceedings of WALCOM 2022 in the Springer LNCS series, vol. 13174, pages 383–395.","year":"2023","publication_status":"published","publisher":"Brown University","department":[{"_id":"UlWa"}]},{"scopus_import":"1","article_processing_charge":"No","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.","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:10.1137/1.9781611977554.ch88.","chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch88.","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:10.1137/1.9781611977554.ch88","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, vol. 2023, pp. 2286–2323.","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch88","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."},"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","page":"2286-2323","date_published":"2023-01-01T00:00:00Z","type":"conference","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."}],"_id":"14344","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2023","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","status":"public","oa_version":"Preprint","publication_identifier":{"isbn":["9781611977554"]},"month":"01","oa":1,"external_id":{"arxiv":["2111.14759"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2111.14759","open_access":"1"}],"quality_controlled":"1","doi":"10.1137/1.9781611977554.ch88","conference":{"start_date":"2023-01-22","location":"Florence, Italy","end_date":"2023-01-25","name":"SODA: Symposium on Discrete Algorithms"},"language":[{"iso":"eng"}],"year":"2023","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"MaKw"}],"publication_status":"published","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"}],"volume":2023,"date_updated":"2023-09-25T09:13:41Z","date_created":"2023-09-17T22:01:10Z"},{"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"month":"03","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/adma.202206110","article_number":"2206110","file_date_updated":"2023-09-26T10:51:56Z","publisher":"Wiley","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","year":"2023","volume":35,"date_updated":"2023-09-26T10:56:46Z","date_created":"2023-03-05T23:01:06Z","author":[{"full_name":"Schamberger, Barbara","last_name":"Schamberger","first_name":"Barbara"},{"last_name":"Ziege","first_name":"Ricardo","full_name":"Ziege, Ricardo"},{"last_name":"Anselme","first_name":"Karine","full_name":"Anselme, Karine"},{"full_name":"Ben Amar, Martine","last_name":"Ben Amar","first_name":"Martine"},{"last_name":"Bykowski","first_name":"Michał","full_name":"Bykowski, Michał"},{"full_name":"Castro, André P.G.","last_name":"Castro","first_name":"André P.G."},{"full_name":"Cipitria, Amaia","first_name":"Amaia","last_name":"Cipitria"},{"last_name":"Coles","first_name":"Rhoslyn A.","full_name":"Coles, Rhoslyn A."},{"full_name":"Dimova, Rumiana","first_name":"Rumiana","last_name":"Dimova"},{"last_name":"Eder","first_name":"Michaela","full_name":"Eder, Michaela"},{"full_name":"Ehrig, Sebastian","first_name":"Sebastian","last_name":"Ehrig"},{"full_name":"Escudero, Luis M.","first_name":"Luis M.","last_name":"Escudero"},{"first_name":"Myfanwy E.","last_name":"Evans","full_name":"Evans, Myfanwy E."},{"first_name":"Paulo R.","last_name":"Fernandes","full_name":"Fernandes, Paulo R."},{"first_name":"Peter","last_name":"Fratzl","full_name":"Fratzl, Peter"},{"full_name":"Geris, Liesbet","last_name":"Geris","first_name":"Liesbet"},{"last_name":"Gierlinger","first_name":"Notburga","full_name":"Gierlinger, Notburga"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Iglič, Aleš","first_name":"Aleš","last_name":"Iglič"},{"full_name":"Kirkensgaard, Jacob J.K.","last_name":"Kirkensgaard","first_name":"Jacob J.K."},{"last_name":"Kollmannsberger","first_name":"Philip","full_name":"Kollmannsberger, Philip"},{"last_name":"Kowalewska","first_name":"Łucja","full_name":"Kowalewska, Łucja"},{"full_name":"Kurniawan, Nicholas A.","last_name":"Kurniawan","first_name":"Nicholas A."},{"full_name":"Papantoniou, Ioannis","first_name":"Ioannis","last_name":"Papantoniou"},{"last_name":"Pieuchot","first_name":"Laurent","full_name":"Pieuchot, Laurent"},{"last_name":"Pires","first_name":"Tiago H.V.","full_name":"Pires, Tiago H.V."},{"first_name":"Lars D.","last_name":"Renner","full_name":"Renner, Lars D."},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"last_name":"Schröder-Turk","first_name":"Gerd E.","full_name":"Schröder-Turk, Gerd E."},{"full_name":"Sengupta, Anupam","first_name":"Anupam","last_name":"Sengupta"},{"last_name":"Sharma","first_name":"Vikas R.","full_name":"Sharma, Vikas R."},{"full_name":"Tagua, Antonio","first_name":"Antonio","last_name":"Tagua"},{"last_name":"Tomba","first_name":"Caterina","full_name":"Tomba, Caterina"},{"full_name":"Trepat, Xavier","last_name":"Trepat","first_name":"Xavier"},{"full_name":"Waters, Sarah L.","last_name":"Waters","first_name":"Sarah L."},{"full_name":"Yeo, Edwina F.","first_name":"Edwina F.","last_name":"Yeo"},{"full_name":"Roschger, Andreas","first_name":"Andreas","last_name":"Roschger"},{"last_name":"Bidan","first_name":"Cécile M.","full_name":"Bidan, Cécile M."},{"last_name":"Dunlop","first_name":"John W.C.","full_name":"Dunlop, John W.C."}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","article_type":"review","citation":{"ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110","ieee":"B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110","chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.","mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023)."},"publication":"Advanced Materials","date_published":"2023-03-29T00:00:00Z","type":"journal_article","issue":"13","abstract":[{"text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.","lang":"eng"}],"intvolume":" 35","ddc":["570"],"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12710","file":[{"creator":"dernst","file_size":2898063,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_AdvancedMaterials_Schamberger.pdf","success":1,"checksum":"5c04d68130e97a0ecd1ca27fbc15a246","date_updated":"2023-09-26T10:51:56Z","date_created":"2023-09-26T10:51:56Z","file_id":"14373","relation":"main_file"}],"oa_version":"Published Version"},{"type":"journal_article","issue":"6","abstract":[{"text":"Coherent flows of self-propelled particles are characterized by vortices and jets that sustain chaotic flows, referred to as active turbulence. Here, we reveal a crossover between defect-free active turbulence and active turbulence laden with topological defects. Interestingly, we show that concurrent to the crossover from defect-free to defect-laden active turbulence is the restoration of the previously broken SO(2) symmetry signaled by the fast decay of the two-point correlations. By stability analyses of the topological charge density field, we provide theoretical insights on the criterion for the crossover to the defect-laden active turbulent state. Despite the distinct symmetry features between these two active turbulence regimes, the flow fluctuations exhibit universal statistical scaling behaviors at large scales, while the spectrum of polarity fluctuations decays exponentially at small length scales compared to the active energy injection length. These findings reveal a dynamical crossover between distinct spatiotemporal organization patterns in polar active matter.","lang":"eng"}],"intvolume":" 8","title":"Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter","status":"public","_id":"14377","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["Fluid Flow and Transfer Processes","Modeling and Simulation","Computational Mechanics"],"scopus_import":"1","article_processing_charge":"No","day":"14","article_type":"original","citation":{"ieee":"B. H. Andersen, J. B. Renaud, J. Rønning, L. Angheluta, and A. Doostmohammadi, “Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter,” Physical Review Fluids, vol. 8, no. 6. American Physical Society, 2023.","apa":"Andersen, B. H., Renaud, J. B., Rønning, J., Angheluta, L., & Doostmohammadi, A. (2023). Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/physrevfluids.8.063101","ista":"Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. 2023. Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. Physical Review Fluids. 8(6), 063101.","ama":"Andersen BH, Renaud JB, Rønning J, Angheluta L, Doostmohammadi A. Symmetry-restoring crossover from defect-free to defect-laden turbulence in polar active matter. Physical Review Fluids. 2023;8(6). doi:10.1103/physrevfluids.8.063101","chicago":"Andersen, Benjamin H., Julian B Renaud, Jonas Rønning, Luiza Angheluta, and Amin Doostmohammadi. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden Turbulence in Polar Active Matter.” Physical Review Fluids. American Physical Society, 2023. https://doi.org/10.1103/physrevfluids.8.063101.","short":"B.H. Andersen, J.B. Renaud, J. Rønning, L. Angheluta, A. Doostmohammadi, Physical Review Fluids 8 (2023).","mla":"Andersen, Benjamin H., et al. “Symmetry-Restoring Crossover from Defect-Free to Defect-Laden Turbulence in Polar Active Matter.” Physical Review Fluids, vol. 8, no. 6, 063101, American Physical Society, 2023, doi:10.1103/physrevfluids.8.063101."},"publication":"Physical Review Fluids","date_published":"2023-06-14T00:00:00Z","article_number":"063101","extern":"1","publisher":"American Physical Society","publication_status":"published","year":"2023","volume":8,"date_created":"2023-09-29T08:46:47Z","date_updated":"2023-10-03T07:25:39Z","author":[{"last_name":"Andersen","first_name":"Benjamin H.","full_name":"Andersen, Benjamin H."},{"first_name":"Julian B","last_name":"Renaud","id":"7af6767d-14eb-11ed-b536-a32449ae867c","full_name":"Renaud, Julian B"},{"full_name":"Rønning, Jonas","first_name":"Jonas","last_name":"Rønning"},{"full_name":"Angheluta, Luiza","last_name":"Angheluta","first_name":"Luiza"},{"first_name":"Amin","last_name":"Doostmohammadi","full_name":"Doostmohammadi, Amin"}],"publication_identifier":{"issn":["2469-990X"]},"month":"06","quality_controlled":"1","external_id":{"arxiv":["2209.10916"]},"main_file_link":[{"url":"https://arxiv.org/abs/2209.10916","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevfluids.8.063101"},{"date_published":"2023-09-22T00:00:00Z","page":"1357-1363","article_type":"original","citation":{"ama":"Gemen J, Church JR, Ruoko T-P, et al. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 2023;381(6664):1357-1363. doi:10.1126/science.adh9059","ista":"Gemen J, Church JR, Ruoko T-P, Durandin N, Białek MJ, Weissenfels M, Feller M, Kazes M, Borin VA, Odaybat M, Kalepu R, Diskin-Posner Y, Oron D, Fuchter MJ, Priimagi A, Schapiro I, Klajn R. 2023. Disequilibrating azoarenes by visible-light sensitization under confinement. Science. 381(6664), 1357–1363.","apa":"Gemen, J., Church, J. R., Ruoko, T.-P., Durandin, N., Białek, M. J., Weissenfels, M., … Klajn, R. (2023). Disequilibrating azoarenes by visible-light sensitization under confinement. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adh9059","ieee":"J. Gemen et al., “Disequilibrating azoarenes by visible-light sensitization under confinement,” Science, vol. 381, no. 6664. American Association for the Advancement of Science, pp. 1357–1363, 2023.","mla":"Gemen, Julius, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science, vol. 381, no. 6664, American Association for the Advancement of Science, 2023, pp. 1357–63, doi:10.1126/science.adh9059.","short":"J. Gemen, J.R. Church, T.-P. Ruoko, N. Durandin, M.J. Białek, M. Weissenfels, M. Feller, M. Kazes, V.A. Borin, M. Odaybat, R. Kalepu, Y. Diskin-Posner, D. Oron, M.J. Fuchter, A. Priimagi, I. Schapiro, R. Klajn, Science 381 (2023) 1357–1363.","chicago":"Gemen, Julius, Jonathan R. Church, Tero-Petri Ruoko, Nikita Durandin, Michał J. Białek, Maren Weissenfels, Moran Feller, et al. “Disequilibrating Azoarenes by Visible-Light Sensitization under Confinement.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adh9059."},"publication":"Science","article_processing_charge":"No","day":"22","scopus_import":"1","oa_version":"Preprint","intvolume":" 381","title":"Disequilibrating azoarenes by visible-light sensitization under confinement","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13340","issue":"6664","abstract":[{"lang":"eng","text":"Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host–photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1126/science.adh9059","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2023-gq2h0","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["1095-9203"]},"month":"09","volume":381,"date_updated":"2023-10-03T08:11:26Z","date_created":"2023-08-01T08:26:15Z","author":[{"last_name":"Gemen","first_name":"Julius","full_name":"Gemen, Julius"},{"full_name":"Church, Jonathan R.","first_name":"Jonathan R.","last_name":"Church"},{"full_name":"Ruoko, Tero-Petri","first_name":"Tero-Petri","last_name":"Ruoko"},{"full_name":"Durandin, Nikita","first_name":"Nikita","last_name":"Durandin"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"full_name":"Weissenfels, Maren","last_name":"Weissenfels","first_name":"Maren"},{"first_name":"Moran","last_name":"Feller","full_name":"Feller, Moran"},{"last_name":"Kazes","first_name":"Miri","full_name":"Kazes, Miri"},{"last_name":"Borin","first_name":"Veniamin A.","full_name":"Borin, Veniamin A."},{"full_name":"Odaybat, Magdalena","first_name":"Magdalena","last_name":"Odaybat"},{"full_name":"Kalepu, Rishir","last_name":"Kalepu","first_name":"Rishir"},{"last_name":"Diskin-Posner","first_name":"Yael","full_name":"Diskin-Posner, Yael"},{"full_name":"Oron, Dan","first_name":"Dan","last_name":"Oron"},{"full_name":"Fuchter, Matthew J.","first_name":"Matthew J.","last_name":"Fuchter"},{"full_name":"Priimagi, Arri","first_name":"Arri","last_name":"Priimagi"},{"first_name":"Igor","last_name":"Schapiro","full_name":"Schapiro, Igor"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"RaKl"}],"publication_status":"published","acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program [European Research Council grants 820008 (Ra.K.) and 101045223 (A.P.) and Marie Skłodowska-Curie grants 812868 (J.G.) and 101022777 (T.-P.R.)], the Academy of Finland [Center of Excellence Programme LIBER grant 346107 (A.P.), Flagship Programme PREIN grant 320165 (A.P.), and Postdoctoral Researcher grant 340103 (T.-P.R.)], Zuckerman STEM Leadership Program Fellowship (J.R.C.), President’s PhD Scholarship (M.O.), and the EPSRC [Established Career Fellowship grant EP/R00188X/1 (M.J.F.)].","year":"2023"},{"abstract":[{"lang":"eng","text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system."}],"issue":"7","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12705","status":"public","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","intvolume":" 158","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2023-02-21T00:00:00Z","publication":"Journal of Chemical Physics","citation":{"chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","ieee":"V. Sorichetti et al., “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” Journal of Chemical Physics, vol. 158, no. 7. American Institute of Physics, 2023.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271","ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 2023;158(7). doi:10.1063/5.0134271"},"article_type":"original","article_number":"074905","author":[{"full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","first_name":"Valerio","last_name":"Sorichetti"},{"full_name":"Ninarello, Andrea","last_name":"Ninarello","first_name":"Andrea"},{"last_name":"Ruiz-Franco","first_name":"José","full_name":"Ruiz-Franco, José"},{"last_name":"Hugouvieux","first_name":"Virginie","full_name":"Hugouvieux, Virginie"},{"full_name":"Zaccarelli, Emanuela","last_name":"Zaccarelli","first_name":"Emanuela"},{"first_name":"Cristian","last_name":"Micheletti","full_name":"Micheletti, Cristian"},{"first_name":"Walter","last_name":"Kob","full_name":"Kob, Walter"},{"full_name":"Rovigatti, Lorenzo","first_name":"Lorenzo","last_name":"Rovigatti"}],"date_created":"2023-03-05T23:01:05Z","date_updated":"2023-10-03T11:31:51Z","volume":158,"acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","year":"2023","pmid":1,"publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"AnSa"}],"month":"02","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"doi":"10.1063/5.0134271","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"oa":1,"external_id":{"arxiv":["2211.04810"],"isi":["000936943800002"],"pmid":["36813705"]},"quality_controlled":"1","isi":1},{"month":"03","publication_identifier":{"eissn":["1572-8102"]},"doi":"10.1007/s10703-023-00411-4","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s10703-023-00411-4","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000946174300001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"ec_funded":1,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen","first_name":"Joost P"},{"last_name":"Mohr","first_name":"Stefanie","full_name":"Mohr, Stefanie"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}],"related_material":{"record":[{"id":"8272","status":"public","relation":"earlier_version"}]},"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-10-03T11:36:13Z","acknowledgement":"Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL.","year":"2023","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"day":"08","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-08T00:00:00Z","publication":"Formal Methods in System Design","citation":{"short":"K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design (2023).","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design, Springer Nature, 2023, doi:10.1007/s10703-023-00411-4.","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” Formal Methods in System Design. Springer Nature, 2023. https://doi.org/10.1007/s10703-023-00411-4.","ama":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. Formal Methods in System Design. 2023. doi:10.1007/s10703-023-00411-4","ieee":"K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” Formal Methods in System Design. Springer Nature, 2023.","apa":"Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., & Winkler, T. (2023). Stochastic games with lexicographic objectives. Formal Methods in System Design. Springer Nature. https://doi.org/10.1007/s10703-023-00411-4","ista":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2023. Stochastic games with lexicographic objectives. Formal Methods in System Design."},"article_type":"original","abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12738","ddc":["000"],"status":"public","title":"Stochastic games with lexicographic objectives"},{"author":[{"full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14274"}]},"date_updated":"2023-10-03T11:42:58Z","date_created":"2023-09-06T08:39:25Z","oa_version":"Published Version","_id":"14279","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","ddc":["570"],"status":"public","publisher":"Zenodo","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"type":"research_data_reference","doi":"10.5281/ZENODO.8133960","date_published":"2023-07-11T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133960"}],"citation":{"ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","mla":"Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960.","short":"M.C. Ucar, (2023).","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960."},"month":"07","day":"11","has_accepted_license":"1","article_processing_charge":"No"},{"issue":"5","abstract":[{"lang":"eng","text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. "}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":803440,"creator":"dernst","access_level":"open_access","file_name":"2023_CommPureMathematics_Cipolloni.pdf","checksum":"8346bc2642afb4ccb7f38979f41df5d9","success":1,"date_created":"2023-10-04T09:21:48Z","date_updated":"2023-10-04T09:21:48Z","relation":"main_file","file_id":"14388"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10405","intvolume":" 76","ddc":["510"],"status":"public","title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034."},"publication":"Communications on Pure and Applied Mathematics","page":"946-1034","article_type":"original","ec_funded":1,"file_date_updated":"2023-10-04T09:21:48Z","author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder"}],"volume":76,"date_updated":"2023-10-04T09:22:55Z","date_created":"2021-12-05T23:01:41Z","year":"2023","acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","publisher":"Wiley","department":[{"_id":"LaEr"}],"publication_status":"published","publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"month":"05","doi":"10.1002/cpa.22028","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"arxiv":["1912.04100"],"isi":["000724652500001"]},"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"author":[{"first_name":"Thomas","last_name":"Graham","full_name":"Graham, Thomas"},{"full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","first_name":"Maria"},{"full_name":"Filar, Jerzy A.","last_name":"Filar","first_name":"Jerzy A."}],"date_created":"2022-02-20T23:01:32Z","date_updated":"2023-10-04T09:24:30Z","volume":13,"acknowledgement":"The authors would like to acknowledge stimulating email discussions with Dr Wayne Lobb of W.A. Lobb LLC on the topic of evolutionary games. We also thank Dr Thomas Taimre for his input to the material in Sect. 3.\r\nThe authors would like to acknowledge partial support from the Australian Research Council under the Discovery grant DP180101602 and support by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"file_date_updated":"2022-02-21T08:54:17Z","ec_funded":1,"doi":"10.1007/s13235-022-00425-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000753777100001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"month":"03","publication_identifier":{"issn":["2153-0785"],"eissn":["2153-0793"]},"oa_version":"Published Version","file":[{"file_size":1890512,"content_type":"application/pdf","creator":"dernst","file_name":"2022_DynamicGamesApplic_Graham.pdf","access_level":"open_access","date_created":"2022-02-21T08:54:17Z","date_updated":"2022-02-21T08:54:17Z","checksum":"cd53b07e96f9030ddb348f305e5b58c7","success":1,"relation":"main_file","file_id":"10781"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10770","title":"Where do mistakes lead? A survey of games with incompetent players","status":"public","ddc":["000"],"intvolume":" 13","abstract":[{"lang":"eng","text":"Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings."}],"type":"journal_article","date_published":"2023-03-01T00:00:00Z","publication":"Dynamic Games and Applications","citation":{"ama":"Graham T, Kleshnina M, Filar JA. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 2023;13:231-264. doi:10.1007/s13235-022-00425-3","ieee":"T. Graham, M. Kleshnina, and J. A. Filar, “Where do mistakes lead? A survey of games with incompetent players,” Dynamic Games and Applications, vol. 13. Springer Nature, pp. 231–264, 2023.","apa":"Graham, T., Kleshnina, M., & Filar, J. A. (2023). Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. Springer Nature. https://doi.org/10.1007/s13235-022-00425-3","ista":"Graham T, Kleshnina M, Filar JA. 2023. Where do mistakes lead? A survey of games with incompetent players. Dynamic Games and Applications. 13, 231–264.","short":"T. Graham, M. Kleshnina, J.A. Filar, Dynamic Games and Applications 13 (2023) 231–264.","mla":"Graham, Thomas, et al. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications, vol. 13, Springer Nature, 2023, pp. 231–64, doi:10.1007/s13235-022-00425-3.","chicago":"Graham, Thomas, Maria Kleshnina, and Jerzy A. Filar. “Where Do Mistakes Lead? A Survey of Games with Incompetent Players.” Dynamic Games and Applications. Springer Nature, 2023. https://doi.org/10.1007/s13235-022-00425-3."},"article_type":"original","page":"231-264","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"}]