--- _id: '11540' abstract: - lang: eng text: Observations have revealed that the star formation rate (SFR) and stellar mass (Mstar) of star-forming galaxies follow a tight relation known as the galaxy main sequence. However, what physical information is encoded in this relation is under debate. Here, we use the EAGLE cosmological hydrodynamical simulation to study the mass dependence, evolution, and origin of scatter in the SFR–Mstar relation. At z = 0, we find that the scatter decreases slightly with stellar mass from 0.35 dex at Mstar ≈ 109 M⊙ to 0.30 dex at Mstar ≳ 1010.5 M⊙. The scatter decreases from z = 0 to z = 5 by 0.05 dex at Mstar ≳ 1010 M⊙ and by 0.15 dex for lower masses. We show that the scatter at z = 0.1 originates from a combination of fluctuations on short time-scales (ranging from 0.2–2 Gyr) that are presumably associated with self-regulation from cooling, star formation, and outflows, but is dominated by long time-scale (∼10 Gyr) variations related to differences in halo formation times. Shorter time-scale fluctuations are relatively more important for lower mass galaxies. At high masses, differences in black hole formation efficiency cause additional scatter, but also diminish the scatter caused by different halo formation times. While individual galaxies cross the main sequence multiple times during their evolution, they fluctuate around tracks associated with their halo properties, i.e. galaxies above/below the main sequence at z = 0.1 tend to have been above/below the main sequence for ≫1 Gyr. acknowledgement: JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013). article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Joop full_name: Schaye, Joop last_name: Schaye citation: ama: Matthee JJ, Schaye J. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 2019;484(1):915-932. doi:10.1093/mnras/stz030 apa: Matthee, J. J., & Schaye, J. (2019). The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz030 chicago: Matthee, Jorryt J, and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz030. ieee: J. J. Matthee and J. Schaye, “The origin of scatter in the star formation rate–stellar mass relation,” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1. Oxford University Press, pp. 915–932, 2019. ista: Matthee JJ, Schaye J. 2019. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 484(1), 915–932. mla: Matthee, Jorryt J., and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1, Oxford University Press, 2019, pp. 915–32, doi:10.1093/mnras/stz030. short: J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society 484 (2019) 915–932. date_created: 2022-07-08T07:48:31Z date_published: 2019-03-01T00:00:00Z date_updated: 2022-08-19T06:42:43Z day: '01' doi: 10.1093/mnras/stz030 extern: '1' external_id: arxiv: - '1805.05956' intvolume: ' 484' issue: '1' keyword: - Space and Planetary Science - 'Astronomy and Astrophysics : galaxies: evolution' - 'galaxies: formation' - 'galaxies: star formation' - 'cosmology: theory' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.05956 month: '03' oa: 1 oa_version: Preprint page: 915-932 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The origin of scatter in the star formation rate–stellar mass relation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 484 year: '2019' ... --- _id: '11616' abstract: - lang: eng text: We present the discovery of HD 221416 b, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. HD 221416 b (HIP 116158, TOI-197) is a bright (V = 8.2 mag), spectroscopically classified subgiant that oscillates with an average frequency of about 430 μHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2 minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (R⋆ = 2.943 ± 0.064 R⊙), mass (M⋆ = 1.212 ± 0.074 M⊙), and age (4.9 ± 1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a "hot Saturn" (Rp = 9.17 ± 0.33 R⊕) with an orbital period of ∼14.3 days, irradiance of F = 343 ± 24 F⊕, and moderate mass (Mp = 60.5 ± 5.7 M⊕) and density (ρp = 0.431 ± 0.062 g cm−3). The properties of HD 221416 b show that the host-star metallicity–planet mass correlation found in sub-Saturns (4–8 R⊕) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ∼15%, HD 221416 b is one of the best characterized Saturn-size planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology. acknowledgement: "The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawai'ian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We thank Andrei Tokovinin for helpful information on the Speckle observations obtained with SOAR. D.H. acknowledges support by the National Aeronautics and Space Administration through the TESS Guest Investigator Program (80NSSC18K1585) and by the National Science Foundation (AST-1717000). A.C. acknowledges support by the National Science Foundation under the Graduate Research Fellowship Program. W.J.C., W.H.B., A.M., O.J.H., and G.R.D. acknowledge support from the Science and Technology Facilities Council and UK Space Agency. H.K. and F.G. acknowledge support from the European Social Fund via the Lithuanian Science Council grant No. 09.3.3-LMT-K-712-01-0103. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (grant DNRF106). A.J. acknowledges support from FONDECYT project 1171208, CONICYT project BASAL AFB-170002, and by the Ministry for the Economy, Development, and Tourism's Programa Iniciativa Científica Milenio through grant IC 120009, awarded to the Millennium Institute of Astrophysics (MAS). R.B. acknowledges support from FONDECYT Post-doctoral Fellowship Project 3180246, and from the Millennium Institute of Astrophysics (MAS). A.M.S. is supported by grants ESP2017-82674-R (MINECO) and SGR2017-1131 (AGAUR). R.A.G. and L.B. acknowledge the support of the PLATO grant from the CNES. The research leading to the presented results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP72007-2013)ERC grant agreement No. 338251 (StellarAges). S.M. acknowledges support from the European Research Council through the SPIRE grant 647383. This work was also supported by FCT (Portugal) through national funds and by FEDER through COMPETE2020 by these grants: UID/FIS/04434/2013 and POCI-01-0145-FEDER-007672, PTDC/FIS-AST/30389/2017, and POCI-01-0145-FEDER-030389. T.L.C. acknowledges support from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 792848 (PULSATION). E.C. is funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 664931. V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B). D.S. acknowledges support from the Australian Research Council. S.B. acknowledges NASA grant NNX16AI09G and NSF grant AST-1514676. T.R.W. acknowledges support from the Australian Research Council through grant DP150100250. A.M. acknowledges support from the ERC Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, G.A. n. 772293). S.M. acknowledges support from the Ramon y Cajal fellowship number RYC-2015-17697. M.S.L. is supported by the Carlsberg Foundation (grant agreement No. CF17-0760). A.M. and P.R. acknowledge support from the HBCSE-NIUS programme. J.K.T. and J.T. acknowledge that support for this work was provided by NASA through Hubble Fellowship grants HST-HF2-51399.001 and HST-HF2-51424.001 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). This project has been supported by the NKFIH K-115709 grant and the Lendület Program of the Hungarian Academy of Sciences, project No. LP2018-7/2018.\r\n\r\nBased on observations made with the Hertzsprung SONG telescope operated on the Spanish Observatorio del Teide on the island of Tenerife by the Aarhus and Copenhagen Universities and by the Instituto de Astrofísica de Canarias. Funding for the TESS mission is provided by NASA's Science Mission directorate. We acknowledge the use of public TESS Alert data from pipelines at the TESS Science Office and at the TESS Science Processing Operations Center. This research has made use of the Exoplanet Follow-up Observation Program website, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. This paper includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST).\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2018), Matplotlib (Hunter 2007), DIAMONDS (Corsaro & De Ridder 2014), isoclassify (Huber et al. 2017), EXOFASTv2 (Eastman 2017), ktransit (Barclay 2018)." article_number: '245' article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Huber, Daniel last_name: Huber - first_name: William J. full_name: Chaplin, William J. last_name: Chaplin - first_name: Ashley full_name: Chontos, Ashley last_name: Chontos - first_name: Hans full_name: Kjeldsen, Hans last_name: Kjeldsen - first_name: Jørgen full_name: Christensen-Dalsgaard, Jørgen last_name: Christensen-Dalsgaard - first_name: Timothy R. full_name: Bedding, Timothy R. last_name: Bedding - first_name: Warrick full_name: Ball, Warrick last_name: Ball - first_name: Rafael full_name: Brahm, Rafael last_name: Brahm - first_name: Nestor full_name: Espinoza, Nestor last_name: Espinoza - first_name: Thomas full_name: Henning, Thomas last_name: Henning - first_name: Andrés full_name: Jordán, Andrés last_name: Jordán - first_name: Paula full_name: Sarkis, Paula last_name: Sarkis - first_name: Emil full_name: Knudstrup, Emil last_name: Knudstrup - first_name: Simon full_name: Albrecht, Simon last_name: Albrecht - first_name: Frank full_name: Grundahl, Frank last_name: Grundahl - first_name: Mads Fredslund full_name: Andersen, Mads Fredslund last_name: Andersen - first_name: Pere L. full_name: Pallé, Pere L. last_name: Pallé - first_name: Ian full_name: Crossfield, Ian last_name: Crossfield - first_name: Benjamin full_name: Fulton, Benjamin last_name: Fulton - first_name: Andrew W. full_name: Howard, Andrew W. last_name: Howard - first_name: Howard T. full_name: Isaacson, Howard T. last_name: Isaacson - first_name: Lauren M. full_name: Weiss, Lauren M. last_name: Weiss - first_name: Rasmus full_name: Handberg, Rasmus last_name: Handberg - first_name: Mikkel N. full_name: Lund, Mikkel N. last_name: Lund - first_name: Aldo M. full_name: Serenelli, Aldo M. last_name: Serenelli - first_name: Jakob full_name: Rørsted Mosumgaard, Jakob last_name: Rørsted Mosumgaard - first_name: Amalie full_name: Stokholm, Amalie last_name: Stokholm - first_name: Allyson full_name: Bieryla, Allyson last_name: Bieryla - first_name: Lars A. full_name: Buchhave, Lars A. last_name: Buchhave - first_name: David W. full_name: Latham, David W. last_name: Latham - first_name: Samuel N. full_name: Quinn, Samuel N. last_name: Quinn - first_name: Eric full_name: Gaidos, Eric last_name: Gaidos - first_name: Teruyuki full_name: Hirano, Teruyuki last_name: Hirano - first_name: George R. full_name: Ricker, George R. last_name: Ricker - first_name: Roland K. full_name: Vanderspek, Roland K. last_name: Vanderspek - first_name: Sara full_name: Seager, Sara last_name: Seager - first_name: Jon M. full_name: Jenkins, Jon M. last_name: Jenkins - first_name: Joshua N. full_name: Winn, Joshua N. last_name: Winn - first_name: H. M. full_name: Antia, H. M. last_name: Antia - first_name: Thierry full_name: Appourchaux, Thierry last_name: Appourchaux - first_name: Sarbani full_name: Basu, Sarbani last_name: Basu - first_name: Keaton J. full_name: Bell, Keaton J. last_name: Bell - first_name: Othman full_name: Benomar, Othman last_name: Benomar - first_name: Alfio full_name: Bonanno, Alfio last_name: Bonanno - first_name: Derek L. full_name: Buzasi, Derek L. last_name: Buzasi - first_name: Tiago L. full_name: Campante, Tiago L. last_name: Campante - first_name: Z. full_name: Çelik Orhan, Z. last_name: Çelik Orhan - first_name: Enrico full_name: Corsaro, Enrico last_name: Corsaro - first_name: Margarida S. full_name: Cunha, Margarida S. last_name: Cunha - first_name: Guy R. full_name: Davies, Guy R. last_name: Davies - first_name: Sebastien full_name: Deheuvels, Sebastien last_name: Deheuvels - first_name: Samuel K. full_name: Grunblatt, Samuel K. last_name: Grunblatt - first_name: Amir full_name: Hasanzadeh, Amir last_name: Hasanzadeh - first_name: Maria Pia full_name: Di Mauro, Maria Pia last_name: Di Mauro - first_name: Rafael full_name: A. García, Rafael last_name: A. García - first_name: Patrick full_name: Gaulme, Patrick last_name: Gaulme - first_name: Léo full_name: Girardi, Léo last_name: Girardi - first_name: Joyce A. full_name: Guzik, Joyce A. last_name: Guzik - first_name: Marc full_name: Hon, Marc last_name: Hon - first_name: Chen full_name: Jiang, Chen last_name: Jiang - first_name: Thomas full_name: Kallinger, Thomas last_name: Kallinger - first_name: Steven D. full_name: Kawaler, Steven D. last_name: Kawaler - first_name: James S. full_name: Kuszlewicz, James S. last_name: Kuszlewicz - first_name: Yveline full_name: Lebreton, Yveline last_name: Lebreton - first_name: Tanda full_name: Li, Tanda last_name: Li - first_name: Miles full_name: Lucas, Miles last_name: Lucas - first_name: Mia S. full_name: Lundkvist, Mia S. last_name: Lundkvist - first_name: Andrew W. full_name: Mann, Andrew W. last_name: Mann - first_name: Stéphane full_name: Mathis, Stéphane last_name: Mathis - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Anwesh full_name: Mazumdar, Anwesh last_name: Mazumdar - first_name: Travis S. full_name: Metcalfe, Travis S. last_name: Metcalfe - first_name: Andrea full_name: Miglio, Andrea last_name: Miglio - first_name: Mário J. P. full_name: F. G. Monteiro, Mário J. P. last_name: F. G. Monteiro - first_name: Benoit full_name: Mosser, Benoit last_name: Mosser - first_name: Anthony full_name: Noll, Anthony last_name: Noll - first_name: Benard full_name: Nsamba, Benard last_name: Nsamba - first_name: Jia Mian full_name: Joel Ong, Jia Mian last_name: Joel Ong - first_name: S. full_name: Örtel, S. last_name: Örtel - first_name: Filipe full_name: Pereira, Filipe last_name: Pereira - first_name: Pritesh full_name: Ranadive, Pritesh last_name: Ranadive - first_name: Clara full_name: Régulo, Clara last_name: Régulo - first_name: Thaíse S. full_name: Rodrigues, Thaíse S. last_name: Rodrigues - first_name: Ian W. full_name: Roxburgh, Ian W. last_name: Roxburgh - first_name: Victor Silva full_name: Aguirre, Victor Silva last_name: Aguirre - first_name: Barry full_name: Smalley, Barry last_name: Smalley - first_name: Mathew full_name: Schofield, Mathew last_name: Schofield - first_name: Sérgio G. full_name: Sousa, Sérgio G. last_name: Sousa - first_name: Keivan G. full_name: Stassun, Keivan G. last_name: Stassun - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Jamie full_name: Tayar, Jamie last_name: Tayar - first_name: Timothy R. full_name: White, Timothy R. last_name: White - first_name: Kuldeep full_name: Verma, Kuldeep last_name: Verma - first_name: Mathieu full_name: Vrard, Mathieu last_name: Vrard - first_name: M. full_name: Yıldız, M. last_name: Yıldız - first_name: David full_name: Baker, David last_name: Baker - first_name: Michaël full_name: Bazot, Michaël last_name: Bazot - first_name: Charles full_name: Beichmann, Charles last_name: Beichmann - first_name: Christoph full_name: Bergmann, Christoph last_name: Bergmann - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Bryson full_name: Cale, Bryson last_name: Cale - first_name: Roberto full_name: Carlino, Roberto last_name: Carlino - first_name: Scott M. full_name: Cartwright, Scott M. last_name: Cartwright - first_name: Jessie L. full_name: Christiansen, Jessie L. last_name: Christiansen - first_name: David R. full_name: Ciardi, David R. last_name: Ciardi - first_name: Orlagh full_name: Creevey, Orlagh last_name: Creevey - first_name: Jason A. full_name: Dittmann, Jason A. last_name: Dittmann - first_name: Jose-Dias Do full_name: Nascimento, Jose-Dias Do last_name: Nascimento - first_name: Vincent Van full_name: Eylen, Vincent Van last_name: Eylen - first_name: Gabor full_name: Fürész, Gabor last_name: Fürész - first_name: Jonathan full_name: Gagné, Jonathan last_name: Gagné - first_name: Peter full_name: Gao, Peter last_name: Gao - first_name: Kosmas full_name: Gazeas, Kosmas last_name: Gazeas - first_name: Frank full_name: Giddens, Frank last_name: Giddens - first_name: Oliver J. full_name: Hall, Oliver J. last_name: Hall - first_name: Saskia full_name: Hekker, Saskia last_name: Hekker - first_name: Michael J. full_name: Ireland, Michael J. last_name: Ireland - first_name: Natasha full_name: Latouf, Natasha last_name: Latouf - first_name: Danny full_name: LeBrun, Danny last_name: LeBrun - first_name: Alan M. full_name: Levine, Alan M. last_name: Levine - first_name: William full_name: Matzko, William last_name: Matzko - first_name: Eva full_name: Natinsky, Eva last_name: Natinsky - first_name: Emma full_name: Page, Emma last_name: Page - first_name: Peter full_name: Plavchan, Peter last_name: Plavchan - first_name: Masoud full_name: Mansouri-Samani, Masoud last_name: Mansouri-Samani - first_name: Sean full_name: McCauliff, Sean last_name: McCauliff - first_name: Susan E. full_name: Mullally, Susan E. last_name: Mullally - first_name: Brendan full_name: Orenstein, Brendan last_name: Orenstein - first_name: Aylin Garcia full_name: Soto, Aylin Garcia last_name: Soto - first_name: Martin full_name: Paegert, Martin last_name: Paegert - first_name: Jennifer L. full_name: van Saders, Jennifer L. last_name: van Saders - first_name: Chloe full_name: Schnaible, Chloe last_name: Schnaible - first_name: David R. full_name: Soderblom, David R. last_name: Soderblom - first_name: Róbert full_name: Szabó, Róbert last_name: Szabó - first_name: Angelle full_name: Tanner, Angelle last_name: Tanner - first_name: C. G. full_name: Tinney, C. G. last_name: Tinney - first_name: Johanna full_name: Teske, Johanna last_name: Teske - first_name: Alexandra full_name: Thomas, Alexandra last_name: Thomas - first_name: Regner full_name: Trampedach, Regner last_name: Trampedach - first_name: Duncan full_name: Wright, Duncan last_name: Wright - first_name: Thomas T. full_name: Yuan, Thomas T. last_name: Yuan - first_name: Farzaneh full_name: Zohrabi, Farzaneh last_name: Zohrabi citation: ama: Huber D, Chaplin WJ, Chontos A, et al. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 2019;157(6). doi:10.3847/1538-3881/ab1488 apa: Huber, D., Chaplin, W. J., Chontos, A., Kjeldsen, H., Christensen-Dalsgaard, J., Bedding, T. R., … Zohrabi, F. (2019). A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. IOP Publishing. https://doi.org/10.3847/1538-3881/ab1488 chicago: Huber, Daniel, William J. Chaplin, Ashley Chontos, Hans Kjeldsen, Jørgen Christensen-Dalsgaard, Timothy R. Bedding, Warrick Ball, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-3881/ab1488. ieee: D. Huber et al., “A hot Saturn orbiting an oscillating late subgiant discovered by TESS,” The Astronomical Journal, vol. 157, no. 6. IOP Publishing, 2019. ista: Huber D et al. 2019. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 157(6), 245. mla: Huber, Daniel, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal, vol. 157, no. 6, 245, IOP Publishing, 2019, doi:10.3847/1538-3881/ab1488. short: D. Huber, W.J. Chaplin, A. Chontos, H. Kjeldsen, J. Christensen-Dalsgaard, T.R. Bedding, W. Ball, R. Brahm, N. Espinoza, T. Henning, A. Jordán, P. Sarkis, E. Knudstrup, S. Albrecht, F. Grundahl, M.F. Andersen, P.L. Pallé, I. Crossfield, B. Fulton, A.W. Howard, H.T. Isaacson, L.M. Weiss, R. Handberg, M.N. Lund, A.M. Serenelli, J. Rørsted Mosumgaard, A. Stokholm, A. Bieryla, L.A. Buchhave, D.W. Latham, S.N. Quinn, E. Gaidos, T. Hirano, G.R. Ricker, R.K. Vanderspek, S. Seager, J.M. Jenkins, J.N. Winn, H.M. Antia, T. Appourchaux, S. Basu, K.J. Bell, O. Benomar, A. Bonanno, D.L. Buzasi, T.L. Campante, Z. Çelik Orhan, E. Corsaro, M.S. Cunha, G.R. Davies, S. Deheuvels, S.K. Grunblatt, A. Hasanzadeh, M.P. Di Mauro, R. A. García, P. Gaulme, L. Girardi, J.A. Guzik, M. Hon, C. Jiang, T. Kallinger, S.D. Kawaler, J.S. Kuszlewicz, Y. Lebreton, T. Li, M. Lucas, M.S. Lundkvist, A.W. Mann, S. Mathis, S. Mathur, A. Mazumdar, T.S. Metcalfe, A. Miglio, M.J.P. F. G. Monteiro, B. Mosser, A. Noll, B. Nsamba, J.M. Joel Ong, S. Örtel, F. Pereira, P. Ranadive, C. Régulo, T.S. Rodrigues, I.W. Roxburgh, V.S. Aguirre, B. Smalley, M. Schofield, S.G. Sousa, K.G. Stassun, D. Stello, J. Tayar, T.R. White, K. Verma, M. Vrard, M. Yıldız, D. Baker, M. Bazot, C. Beichmann, C. Bergmann, L.A. Bugnet, B. Cale, R. Carlino, S.M. Cartwright, J.L. Christiansen, D.R. Ciardi, O. Creevey, J.A. Dittmann, J.-D.D. Nascimento, V.V. Eylen, G. Fürész, J. Gagné, P. Gao, K. Gazeas, F. Giddens, O.J. Hall, S. Hekker, M.J. Ireland, N. Latouf, D. LeBrun, A.M. Levine, W. Matzko, E. Natinsky, E. Page, P. Plavchan, M. Mansouri-Samani, S. McCauliff, S.E. Mullally, B. Orenstein, A.G. Soto, M. Paegert, J.L. van Saders, C. Schnaible, D.R. Soderblom, R. Szabó, A. Tanner, C.G. Tinney, J. Teske, A. Thomas, R. Trampedach, D. Wright, T.T. Yuan, F. Zohrabi, The Astronomical Journal 157 (2019). date_created: 2022-07-18T14:29:07Z date_published: 2019-05-30T00:00:00Z date_updated: 2022-08-22T07:38:34Z day: '30' doi: 10.3847/1538-3881/ab1488 extern: '1' external_id: arxiv: - '1901.01643' intvolume: ' 157' issue: '6' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1901.01643 month: '05' oa: 1 oa_version: Preprint publication: The Astronomical Journal publication_identifier: issn: - 0004-6256 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: A hot Saturn orbiting an oscillating late subgiant discovered by TESS type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 157 year: '2019' ... --- _id: '11613' abstract: - lang: eng text: Over 2,000 stars were observed for 1 month with a high enough cadence in order to look for acoustic modes during the survey phase of the Kepler mission. Solar-like oscillations have been detected in about 540 stars. The question of why no oscillations were detected in the remaining stars is still open. Previous works explained the non-detection of modes with the high level of magnetic activity of the stars. However, the sample of stars studied contained some classical pulsators and red giants that could have biased the results. In this work, we revisit this analysis on a cleaner sample of main-sequence solar-like stars that consists of 1,014 stars. First we compute the predicted amplitude of the modes of that sample and for the stars with detected oscillation and compare it to the noise at high frequency in the power spectrum. We find that the stars with detected modes have an amplitude to noise ratio larger than 0.94. We measure reliable rotation periods and the associated photometric magnetic index for 684 stars out of the full sample and in particular for 323 stars where the amplitude of the modes is predicted to be high enough to be detected. We find that among these 323 stars 32% of them have a level of magnetic activity larger than the Sun during its maximum activity, explaining the non-detection of acoustic modes. Interestingly, magnetic activity cannot be the primary reason responsible for the absence of detectable modes in the remaining 68% of the stars without acoustic modes detected and with reliable rotation periods. Thus, we investigate metallicity, inclination angle of the rotation axis, and binarity as possible causes of low mode amplitudes. Using spectroscopic observations for a subsample, we find that a low metallicity could be the reason for suppressed modes. No clear correlation with binarity nor inclination is found. We also derive the lower limit for our photometric activity index (of 20–30 ppm) below which rotation and magnetic activity are not detected. Finally, with our analysis we conclude that stars with a photometric activity index larger than 2,000 ppm have 98.3% probability of not having oscillations detected. acknowledgement: This paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate. Some of the data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Partly Based on observations obtained with the HERMES spectrograph on the Mercator Telescope, which was supported by the Research Foundation—Flanders (FWO), Belgium, the Research Council of KU Leuven, Belgium, the Fonds National de la Recherche Scientifique (F.R.S.-FNRS), Belgium, the Royal Observatory of Belgium, the Observatoire de Genève, Switzerland, and the Thüringer Landessternwarte Tautenburg, Germany. SM acknowledges support by the National Aeronautics and Space Administration under Grant NNX15AF13G, by the National Science Foundation grant AST-1411685, and the Ramon y Cajal fellowship number RYC-2015-17697. RG acknowledges the support from PLATO and GOLF CNES grants. ÂS acknowledges the support from National Aeronautics and Space Administration under Grant NNX17AF27G. PB acknowledges the support of the MINECO under the fellowship program Juan de la Cierva Incorporacion (IJCI-2015-26034). article_number: '46' article_processing_charge: No article_type: original author: - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Rafael A. full_name: García, Rafael A. last_name: García - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: Ângela R.G. full_name: Santos, Ângela R.G. last_name: Santos - first_name: Netsha full_name: Santiago, Netsha last_name: Santiago - first_name: Paul G. full_name: Beck, Paul G. last_name: Beck citation: ama: Mathur S, García RA, Bugnet LA, Santos ÂRG, Santiago N, Beck PG. Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. 2019;6. doi:10.3389/fspas.2019.00046 apa: Mathur, S., García, R. A., Bugnet, L. A., Santos, Â. R. G., Santiago, N., & Beck, P. G. (2019). Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. Frontiers Media. https://doi.org/10.3389/fspas.2019.00046 chicago: Mathur, Savita, Rafael A. García, Lisa Annabelle Bugnet, Ângela R.G. Santos, Netsha Santiago, and Paul G. Beck. “Revisiting the Impact of Stellar Magnetic Activity on the Detectability of Solar-like Oscillations by Kepler.” Frontiers in Astronomy and Space Sciences. Frontiers Media, 2019. https://doi.org/10.3389/fspas.2019.00046. ieee: S. Mathur, R. A. García, L. A. Bugnet, Â. R. G. Santos, N. Santiago, and P. G. Beck, “Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler,” Frontiers in Astronomy and Space Sciences, vol. 6. Frontiers Media, 2019. ista: Mathur S, García RA, Bugnet LA, Santos ÂRG, Santiago N, Beck PG. 2019. Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler. Frontiers in Astronomy and Space Sciences. 6, 46. mla: Mathur, Savita, et al. “Revisiting the Impact of Stellar Magnetic Activity on the Detectability of Solar-like Oscillations by Kepler.” Frontiers in Astronomy and Space Sciences, vol. 6, 46, Frontiers Media, 2019, doi:10.3389/fspas.2019.00046. short: S. Mathur, R.A. García, L.A. Bugnet, Â.R.G. Santos, N. Santiago, P.G. Beck, Frontiers in Astronomy and Space Sciences 6 (2019). date_created: 2022-07-18T14:00:36Z date_published: 2019-07-10T00:00:00Z date_updated: 2022-08-22T07:29:55Z day: '10' doi: 10.3389/fspas.2019.00046 extern: '1' external_id: arxiv: - '1907.01415' intvolume: ' 6' keyword: - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.01415 month: '07' oa: 1 oa_version: Preprint publication: Frontiers in Astronomy and Space Sciences publication_identifier: eissn: - 2296-987X publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2019' ... --- _id: '11615' abstract: - lang: eng text: The recently published Kepler mission Data Release 25 (DR25) reported on ∼197 000 targets observed during the mission. Despite this, no wide search for red giants showing solar-like oscillations have been made across all stars observed in Kepler’s long-cadence mode. In this work, we perform this task using custom apertures on the Kepler pixel files and detect oscillations in 21 914 stars, representing the largest sample of solar-like oscillating stars to date. We measure their frequency at maximum power, νmax, down to νmax≃4μHz and obtain log (g) estimates with a typical uncertainty below 0.05 dex, which is superior to typical measurements from spectroscopy. Additionally, the νmax distribution of our detections show good agreement with results from a simulated model of the Milky Way, with a ratio of observed to predicted stars of 0.992 for stars with 10<νmax<270μHz. Among our red giant detections, we find 909 to be dwarf/subgiant stars whose flux signal is polluted by a neighbouring giant as a result of using larger photometric apertures than those used by the NASA Kepler science processing pipeline. We further find that only 293 of the polluting giants are known Kepler targets. The remainder comprises over 600 newly identified oscillating red giants, with many expected to belong to the Galactic halo, serendipitously falling within the Kepler pixel files of targeted stars. acknowledgement: Funding for this Discovery mission is provided by NASA’s Science mission Directorate. We thank the entire Kepler team without whom this investigation would not be possible. DS is the recipient of an Australian Research Council Future Fellowship (project number FT1400147). RAG acknowledges the support from CNES. SM acknowledges support from NASA grant NNX15AF13G, NSF grant AST-1411685, and the Ramon y Cajal fellowship number RYC-2015-17697. ILC acknowledges scholarship support from the University of Sydney. We would like to thank Nicholas Barbara and Timothy Bedding for providing us with a list of variable stars that helped to validate a number of detections in this study. We also thank the group at the University of Sydney for fruitful discussions. Finally, we gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research. article_processing_charge: No article_type: original author: - first_name: Marc full_name: Hon, Marc last_name: Hon - first_name: Dennis full_name: Stello, Dennis last_name: Stello - first_name: Rafael A full_name: García, Rafael A last_name: García - first_name: Savita full_name: Mathur, Savita last_name: Mathur - first_name: Sanjib full_name: Sharma, Sanjib last_name: Sharma - first_name: Isabel L full_name: Colman, Isabel L last_name: Colman - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 citation: ama: Hon M, Stello D, García RA, et al. A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. 2019;485(4):5616-5630. doi:10.1093/mnras/stz622 apa: Hon, M., Stello, D., García, R. A., Mathur, S., Sharma, S., Colman, I. L., & Bugnet, L. A. (2019). A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz622 chicago: Hon, Marc, Dennis Stello, Rafael A García, Savita Mathur, Sanjib Sharma, Isabel L Colman, and Lisa Annabelle Bugnet. “A Search for Red Giant Solar-like Oscillations in All Kepler Data.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz622. ieee: M. Hon et al., “A search for red giant solar-like oscillations in all Kepler data,” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 4. Oxford University Press, pp. 5616–5630, 2019. ista: Hon M, Stello D, García RA, Mathur S, Sharma S, Colman IL, Bugnet LA. 2019. A search for red giant solar-like oscillations in all Kepler data. Monthly Notices of the Royal Astronomical Society. 485(4), 5616–5630. mla: Hon, Marc, et al. “A Search for Red Giant Solar-like Oscillations in All Kepler Data.” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 4, Oxford University Press, 2019, pp. 5616–30, doi:10.1093/mnras/stz622. short: M. Hon, D. Stello, R.A. García, S. Mathur, S. Sharma, I.L. Colman, L.A. Bugnet, Monthly Notices of the Royal Astronomical Society 485 (2019) 5616–5630. date_created: 2022-07-18T14:26:03Z date_published: 2019-06-01T00:00:00Z date_updated: 2022-08-22T07:35:19Z day: '01' doi: 10.1093/mnras/stz622 extern: '1' external_id: arxiv: - '1903.00115' intvolume: ' 485' issue: '4' keyword: - Space and Planetary Science - Astronomy and Astrophysics - asteroseismology - 'methods: data analysis' - 'techniques: image processing' - 'stars: oscillations' - 'stars: statistics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.00115 month: '06' oa: 1 oa_version: Preprint page: 5616-5630 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: A search for red giant solar-like oscillations in all Kepler data type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 485 year: '2019' ... --- _id: '11614' abstract: - lang: eng text: The NASA Transiting Exoplanet Survey Satellite (TESS) is about to provide full-frame images of almost the entire sky. The amount of stellar data to be analysed represents hundreds of millions stars, which is several orders of magnitude more than the number of stars observed by the Convection, Rotation and planetary Transits satellite (CoRoT), and NASA Kepler and K2 missions. We aim at automatically classifying the newly observed stars with near real-time algorithms to better guide the subsequent detailed studies. In this paper, we present a classification algorithm built to recognise solar-like pulsators among classical pulsators. This algorithm relies on the global amount of power contained in the power spectral density (PSD), also known as the flicker in spectral power density (FliPer). Because each type of pulsating star has a characteristic background or pulsation pattern, the shape of the PSD at different frequencies can be used to characterise the type of pulsating star. The FliPer classifier (FliPerClass) uses different FliPer parameters along with the effective temperature as input parameters to feed a ML algorithm in order to automatically classify the pulsating stars observed by TESS. Using noisy TESS-simulated data from the TESS Asteroseismic Science Consortium (TASC), we classify pulsators with a 98% accuracy. Among them, solar-like pulsating stars are recognised with a 99% accuracy, which is of great interest for a further seismic analysis of these stars, which are like our Sun. Similar results are obtained when we trained our classifier and applied it to 27-day subsets of real Kepler data. FliPerClass is part of the large TASC classification pipeline developed by the TESS Data for Asteroseismology (T’DA) classification working group. acknowledgement: We thank the enitre T’DA team for useful comments and discussions, in particular Andrew Tkachenko. We also acknowledge Marc Hon, Keaton Bell, and James Kuszlewicz for useful comments on the manuscript. L.B. and R.A.G. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges support by the Ramon y Cajal fellowship number RYC-2015-17697. O.J.H. and B.M.R. acknowledge the support of the UK Science and Technology Facilities Council (STFC). M.N.L. acknowledges the support of the ESA PRODEX programme (PEA 4000119301). Funding for the Stellar Astrophysics Centre is provided by the Danish National Research Foundation (Grant DNRF106). article_number: A79 article_processing_charge: No article_type: original author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: R. A. full_name: García, R. A. last_name: García - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: G. R. full_name: Davies, G. R. last_name: Davies - first_name: O. J. full_name: Hall, O. J. last_name: Hall - first_name: M. N. full_name: Lund, M. N. last_name: Lund - first_name: B. M. full_name: Rendle, B. M. last_name: Rendle citation: ama: 'Bugnet LA, García RA, Mathur S, et al. FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201834780' apa: 'Bugnet, L. A., García, R. A., Mathur, S., Davies, G. R., Hall, O. J., Lund, M. N., & Rendle, B. M. (2019). FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. EDP Science. https://doi.org/10.1051/0004-6361/201834780' chicago: 'Bugnet, Lisa Annabelle, R. A. García, S. Mathur, G. R. Davies, O. J. Hall, M. N. Lund, and B. M. Rendle. “FliPerClass: In Search of Solar-like Pulsators among TESS Targets.” Astronomy & Astrophysics. EDP Science, 2019. https://doi.org/10.1051/0004-6361/201834780.' ieee: 'L. A. Bugnet et al., “FliPerClass: In search of solar-like pulsators among TESS targets,” Astronomy & Astrophysics, vol. 624. EDP Science, 2019.' ista: 'Bugnet LA, García RA, Mathur S, Davies GR, Hall OJ, Lund MN, Rendle BM. 2019. FliPerClass: In search of solar-like pulsators among TESS targets. Astronomy & Astrophysics. 624, A79.' mla: 'Bugnet, Lisa Annabelle, et al. “FliPerClass: In Search of Solar-like Pulsators among TESS Targets.” Astronomy & Astrophysics, vol. 624, A79, EDP Science, 2019, doi:10.1051/0004-6361/201834780.' short: L.A. Bugnet, R.A. García, S. Mathur, G.R. Davies, O.J. Hall, M.N. Lund, B.M. Rendle, Astronomy & Astrophysics 624 (2019). date_created: 2022-07-18T14:13:34Z date_published: 2019-04-19T00:00:00Z date_updated: 2022-08-22T07:32:51Z day: '19' doi: 10.1051/0004-6361/201834780 extern: '1' external_id: arxiv: - '1902.09854' intvolume: ' 624' keyword: - Space and Planetary Science - Astronomy and Astrophysics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.09854 month: '04' oa: 1 oa_version: Preprint publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Science quality_controlled: '1' scopus_import: '1' status: public title: 'FliPerClass: In search of solar-like pulsators among TESS targets' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 624 year: '2019' ... --- _id: '11623' abstract: - lang: eng text: Brightness variations due to dark spots on the stellar surface encode information about stellar surface rotation and magnetic activity. In this work, we analyze the Kepler long-cadence data of 26,521 main-sequence stars of spectral types M and K in order to measure their surface rotation and photometric activity level. Rotation-period estimates are obtained by the combination of a wavelet analysis and autocorrelation function of the light curves. Reliable rotation estimates are determined by comparing the results from the different rotation diagnostics and four data sets. We also measure the photometric activity proxy Sph using the amplitude of the flux variations on an appropriate timescale. We report rotation periods and photometric activity proxies for about 60% of the sample, including 4431 targets for which McQuillan et al. did not report a rotation period. For the common targets with rotation estimates in this study and in McQuillan et al., our rotation periods agree within 99%. In this work, we also identify potential polluters, such as misclassified red giants and classical pulsator candidates. Within the parameter range we study, there is a mild tendency for hotter stars to have shorter rotation periods. The photometric activity proxy spans a wider range of values with increasing effective temperature. The rotation period and photometric activity proxy are also related, with Sph being larger for fast rotators. Similar to McQuillan et al., we find a bimodal distribution of rotation periods. acknowledgement: "The authors thank Róbert Szabó Paul G. Beck, Katrien Kolenberg, and Isabel L. Colman for helping on the classification of stars. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the National Aeronautics and Space Administration (NASA) Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. A.R.G.S. acknowledges the support from NASA under grant NNX17AF27G. R.A.G. and L.B. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges the support from the Ramon y Cajal fellowship number RYC-2015-17697. T.S.M. acknowledges support from a Visiting Fellowship at the Max Planck Institute for Solar System Research. This research has made use of the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program.\r\n\r\nSoftware: KADACS (García et al. 2011), NumPy (van der Walt et al. 2011), SciPy (Jones et al. 2001), Matplotlib (Hunter 2007).\r\n\r\nFacilities: MAST - , Kepler Eclipsing Binary Catalog - , Exoplanet Archive. -" article_number: '21' article_processing_charge: No article_type: original author: - first_name: A. R. G. full_name: Santos, A. R. G. last_name: Santos - first_name: R. A. full_name: García, R. A. last_name: García - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: J. L. full_name: van Saders, J. L. last_name: van Saders - first_name: T. S. full_name: Metcalfe, T. S. last_name: Metcalfe - first_name: G. V. A. full_name: Simonian, G. V. A. last_name: Simonian - first_name: M. H. full_name: Pinsonneault, M. H. last_name: Pinsonneault citation: ama: Santos ARG, García RA, Mathur S, et al. Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. 2019;244(1). doi:10.3847/1538-4365/ab3b56 apa: Santos, A. R. G., García, R. A., Mathur, S., Bugnet, L. A., van Saders, J. L., Metcalfe, T. S., … Pinsonneault, M. H. (2019). Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. IOP Publishing. https://doi.org/10.3847/1538-4365/ab3b56 chicago: Santos, A. R. G., R. A. García, S. Mathur, Lisa Annabelle Bugnet, J. L. van Saders, T. S. Metcalfe, G. V. A. Simonian, and M. H. Pinsonneault. “Surface Rotation and Photometric Activity for Kepler Targets. I. M and K Main-Sequence Stars.” The Astrophysical Journal Supplement Series. IOP Publishing, 2019. https://doi.org/10.3847/1538-4365/ab3b56. ieee: A. R. G. Santos et al., “Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars,” The Astrophysical Journal Supplement Series, vol. 244, no. 1. IOP Publishing, 2019. ista: Santos ARG, García RA, Mathur S, Bugnet LA, van Saders JL, Metcalfe TS, Simonian GVA, Pinsonneault MH. 2019. Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars. The Astrophysical Journal Supplement Series. 244(1), 21. mla: Santos, A. R. G., et al. “Surface Rotation and Photometric Activity for Kepler Targets. I. M and K Main-Sequence Stars.” The Astrophysical Journal Supplement Series, vol. 244, no. 1, 21, IOP Publishing, 2019, doi:10.3847/1538-4365/ab3b56. short: A.R.G. Santos, R.A. García, S. Mathur, L.A. Bugnet, J.L. van Saders, T.S. Metcalfe, G.V.A. Simonian, M.H. Pinsonneault, The Astrophysical Journal Supplement Series 244 (2019). date_created: 2022-07-19T09:21:58Z date_published: 2019-09-19T00:00:00Z date_updated: 2022-08-22T08:10:38Z day: '19' doi: 10.3847/1538-4365/ab3b56 extern: '1' external_id: arxiv: - '1908.05222' intvolume: ' 244' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'methods: data analysis' - 'stars: activity' - 'stars: low-mass' - 'stars: rotation' - starspots - 'techniques: photometric' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.05222 month: '09' oa: 1 oa_version: Preprint publication: The Astrophysical Journal Supplement Series publication_identifier: issn: - 0067-0049 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 244 year: '2019' ... --- _id: '11627' abstract: - lang: eng text: 'For a solar-like star, the surface rotation evolves with time, allowing in principle to estimate the age of a star from its surface rotation period. Here we are interested in measuring surface rotation periods of solar-like stars observed by the NASA mission Kepler. Different methods have been developed to track rotation signals in Kepler photometric light curves: time-frequency analysis based on wavelet techniques, autocorrelation and composite spectrum. We use the learning abilities of random forest classifiers to take decisions during two crucial steps of the analysis. First, given some input parameters, we discriminate the considered Kepler targets between rotating MS stars, non-rotating MS stars, red giants, binaries and pulsators. We then use a second classifier only on the MS rotating targets to decide the best data analysis treatment.' article_number: '1906.09609' article_processing_charge: No author: - first_name: S. N. full_name: Breton, S. N. last_name: Breton - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: A. R. G. full_name: Santos, A. R. G. last_name: Santos - first_name: A. Le full_name: Saux, A. Le last_name: Saux - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: P. L. full_name: Palle, P. L. last_name: Palle - first_name: R. A. full_name: Garcia, R. A. last_name: Garcia citation: ama: Breton SN, Bugnet LA, Santos ARG, et al. Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv. doi:10.48550/arXiv.1906.09609 apa: Breton, S. N., Bugnet, L. A., Santos, A. R. G., Saux, A. L., Mathur, S., Palle, P. L., & Garcia, R. A. (n.d.). Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv. https://doi.org/10.48550/arXiv.1906.09609 chicago: Breton, S. N., Lisa Annabelle Bugnet, A. R. G. Santos, A. Le Saux, S. Mathur, P. L. Palle, and R. A. Garcia. “Determining Surface Rotation Periods of Solar-like Stars Observed by the Kepler Mission Using Machine Learning Techniques.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1906.09609. ieee: S. N. Breton et al., “Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques,” arXiv. . ista: Breton SN, Bugnet LA, Santos ARG, Saux AL, Mathur S, Palle PL, Garcia RA. Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques. arXiv, 1906.09609. mla: Breton, S. N., et al. “Determining Surface Rotation Periods of Solar-like Stars Observed by the Kepler Mission Using Machine Learning Techniques.” ArXiv, 1906.09609, doi:10.48550/arXiv.1906.09609. short: S.N. Breton, L.A. Bugnet, A.R.G. Santos, A.L. Saux, S. Mathur, P.L. Palle, R.A. Garcia, ArXiv (n.d.). date_created: 2022-07-20T11:18:53Z date_published: 2019-06-23T00:00:00Z date_updated: 2022-08-22T08:16:53Z day: '23' doi: 10.48550/arXiv.1906.09609 extern: '1' external_id: arxiv: - '1906.09609' keyword: - asteroseismology - rotation - solar-like stars - kepler - machine learning - random forest language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.09609 month: '06' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11630' abstract: - lang: eng text: 'The second mission of NASA’s Kepler satellite, K2, has collected hundreds of thousands of lightcurves for stars close to the ecliptic plane. This new sample could increase the number of known pulsating stars and then improve our understanding of those stars. For the moment only a few stars have been properly classified and published. In this work, we present a method to automaticly classify K2 pulsating stars using a Machine Learning technique called Random Forest. The objective is to sort out the stars in four classes: red giant (RG), main-sequence Solar-like stars (SL), classical pulsators (PULS) and Other. To do this we use the effective temperatures and the luminosities of the stars as well as the FliPer features, that measures the amount of power contained in the power spectral density. The classifier now retrieves the right classification for more than 80% of the stars.' article_number: '1906.09611' article_processing_charge: No author: - first_name: A. Le full_name: Saux, A. Le last_name: Saux - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: S. N. full_name: Breton, S. N. last_name: Breton - first_name: R. A. full_name: Garcia, R. A. last_name: Garcia citation: ama: Saux AL, Bugnet LA, Mathur S, Breton SN, Garcia RA. Automatic classification of K2 pulsating stars using machine learning techniques. arXiv. doi:10.48550/arXiv.1906.09611 apa: Saux, A. L., Bugnet, L. A., Mathur, S., Breton, S. N., & Garcia, R. A. (n.d.). Automatic classification of K2 pulsating stars using machine learning techniques. arXiv. https://doi.org/10.48550/arXiv.1906.09611 chicago: Saux, A. Le, Lisa Annabelle Bugnet, S. Mathur, S. N. Breton, and R. A. Garcia. “Automatic Classification of K2 Pulsating Stars Using Machine Learning Techniques.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1906.09611. ieee: A. L. Saux, L. A. Bugnet, S. Mathur, S. N. Breton, and R. A. Garcia, “Automatic classification of K2 pulsating stars using machine learning techniques,” arXiv. . ista: Saux AL, Bugnet LA, Mathur S, Breton SN, Garcia RA. Automatic classification of K2 pulsating stars using machine learning techniques. arXiv, 1906.09611. mla: Saux, A. Le, et al. “Automatic Classification of K2 Pulsating Stars Using Machine Learning Techniques.” ArXiv, 1906.09611, doi:10.48550/arXiv.1906.09611. short: A.L. Saux, L.A. Bugnet, S. Mathur, S.N. Breton, R.A. Garcia, ArXiv (n.d.). date_created: 2022-07-21T06:57:10Z date_published: 2019-06-23T00:00:00Z date_updated: 2022-08-22T08:20:29Z day: '23' doi: 10.48550/arXiv.1906.09611 extern: '1' external_id: arxiv: - '1906.09611' keyword: - asteroseismology - methods - data analysis - thecniques - machine learning - stars - oscillations language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1906.09611 month: '06' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Automatic classification of K2 pulsating stars using machine learning techniques type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11826' abstract: - lang: eng text: "The diameter, radius and eccentricities are natural graph parameters. While these problems have been studied extensively, there are no known dynamic algorithms for them beyond the ones that follow from trivial recomputation after each update or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally intensive. This is the situation for dynamic approximation algorithms as well, and even if only edge insertions or edge deletions need to be supported.\r\nThis paper provides a comprehensive study of the dynamic approximation of Diameter, Radius and Eccentricities, providing both conditional lower bounds, and new algorithms whose bounds are optimal under popular hypotheses in fine-grained complexity. Some of the highlights include:\r\n- Under popular hardness hypotheses, there can be no significantly better fully dynamic approximation algorithms than recomputing the answer after each update, or maintaining full APSP.\r\n- Nearly optimal partially dynamic (incremental/decremental) algorithms can be achieved via efficient reductions to (incremental/decremental) maintenance of Single-Source Shortest Paths. For instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2. This nearly matches the static 3/2-approximation algorithm for the problem that is known to be conditionally optimal." alternative_title: - LIPIcs article_number: '13' article_processing_charge: No author: - first_name: Bertie full_name: Ancona, Bertie last_name: Ancona - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Liam full_name: Roditty, Liam last_name: Roditty - first_name: Virginia Vassilevska full_name: Williams, Virginia Vassilevska last_name: Williams - first_name: Nicole full_name: Wein, Nicole last_name: Wein citation: ama: 'Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. Algorithms and hardness for diameter in dynamic graphs. In: 46th International Colloquium on Automata, Languages, and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ICALP.2019.13' apa: 'Ancona, B., Henzinger, M. H., Roditty, L., Williams, V. V., & Wein, N. (2019). Algorithms and hardness for diameter in dynamic graphs. In 46th International Colloquium on Automata, Languages, and Programming (Vol. 132). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.13' chicago: Ancona, Bertie, Monika H Henzinger, Liam Roditty, Virginia Vassilevska Williams, and Nicole Wein. “Algorithms and Hardness for Diameter in Dynamic Graphs.” In 46th International Colloquium on Automata, Languages, and Programming, Vol. 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.13. ieee: B. Ancona, M. H. Henzinger, L. Roditty, V. V. Williams, and N. Wein, “Algorithms and hardness for diameter in dynamic graphs,” in 46th International Colloquium on Automata, Languages, and Programming, Patras, Greece, 2019, vol. 132. ista: 'Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. 2019. Algorithms and hardness for diameter in dynamic graphs. 46th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 132, 13.' mla: Ancona, Bertie, et al. “Algorithms and Hardness for Diameter in Dynamic Graphs.” 46th International Colloquium on Automata, Languages, and Programming, vol. 132, 13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ICALP.2019.13. short: B. Ancona, M.H. Henzinger, L. Roditty, V.V. Williams, N. Wein, in:, 46th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-07-12 location: Patras, Greece name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2019-07-09 date_created: 2022-08-12T08:14:51Z date_published: 2019-07-04T00:00:00Z date_updated: 2023-02-16T10:48:24Z day: '04' doi: 10.4230/LIPICS.ICALP.2019.13 extern: '1' external_id: arxiv: - '811.12527' intvolume: ' 132' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ICALP.2019.13 month: '07' oa: 1 oa_version: Published Version publication: 46th International Colloquium on Automata, Languages, and Programming publication_identifier: isbn: - 978-3-95977-109-2 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Algorithms and hardness for diameter in dynamic graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 132 year: '2019' ... --- _id: '11850' abstract: - lang: eng text: 'Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Stefan full_name: Neumann, Stefan last_name: Neumann - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid citation: ama: 'Henzinger MH, Neumann S, Schmid S. Efficient distributed workload (re-)embedding. In: SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. Association for Computing Machinery; 2019:43–44. doi:10.1145/3309697.3331503' apa: 'Henzinger, M. H., Neumann, S., & Schmid, S. (2019). Efficient distributed workload (re-)embedding. In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems (pp. 43–44). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3309697.3331503' chicago: 'Henzinger, Monika H, Stefan Neumann, and Stefan Schmid. “Efficient Distributed Workload (Re-)Embedding.” In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, 43–44. Association for Computing Machinery, 2019. https://doi.org/10.1145/3309697.3331503.' ieee: 'M. H. Henzinger, S. Neumann, and S. Schmid, “Efficient distributed workload (re-)embedding,” in SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Phoenix, AZ, United States, 2019, pp. 43–44.' ista: 'Henzinger MH, Neumann S, Schmid S. 2019. Efficient distributed workload (re-)embedding. SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 43–44.' mla: 'Henzinger, Monika H., et al. “Efficient Distributed Workload (Re-)Embedding.” SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44, doi:10.1145/3309697.3331503.' short: 'M.H. Henzinger, S. Neumann, S. Schmid, in:, SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44.' conference: end_date: 2019-06-28 location: Phoenix, AZ, United States name: 'SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems' start_date: 2019-06-24 date_created: 2022-08-16T07:14:57Z date_published: 2019-06-20T00:00:00Z date_updated: 2023-02-17T09:41:45Z day: '20' doi: 10.1145/3309697.3331503 extern: '1' external_id: arxiv: - '1904.05474' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.05474 month: '06' oa: 1 oa_version: Preprint page: 43–44 publication: 'SIGMETRICS''19: International Conference on Measurement and Modeling of Computer Systems' publication_identifier: isbn: - 978-1-4503-6678-6 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Efficient distributed workload (re-)embedding type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11847' abstract: - lang: eng text: This paper serves as a user guide to the Vienna graph clustering framework. We review our general memetic algorithm, VieClus, to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. After giving a description of the algorithms employed, we establish the connection of the graph clustering problem to protein–protein interaction networks and moreover give a description on how the software can be used, what file formats are expected, and how this can be used to find functional groups in protein–protein interaction networks. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Sonja full_name: Biedermann, Sonja last_name: Biedermann - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Bernhard full_name: Schuster, Bernhard last_name: Schuster citation: ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering. In: Canzar S, Rojas Ringeling F, eds. Protein-Protein Interaction Networks. Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:10.1007/978-1-4939-9873-9_16' apa: Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2019). Vienna Graph Clustering. In S. Canzar & F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks (Vol. 2074, pp. 215–231). Springer Nature. https://doi.org/10.1007/978-1-4939-9873-9_16 chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Vienna Graph Clustering.” In Protein-Protein Interaction Networks, edited by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature, 2019. https://doi.org/10.1007/978-1-4939-9873-9_16. ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph Clustering,” in Protein-Protein Interaction Networks, vol. 2074, S. Canzar and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231. ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering. In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074, 215–231.' mla: Biedermann, Sonja, et al. “Vienna Graph Clustering.” Protein-Protein Interaction Networks, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074, Springer Nature, 2019, pp. 215–231, doi:10.1007/978-1-4939-9873-9_16. short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature, 2019, pp. 215–231. date_created: 2022-08-16T06:54:48Z date_published: 2019-10-04T00:00:00Z date_updated: 2023-02-17T09:34:26Z day: '04' doi: 10.1007/978-1-4939-9873-9_16 editor: - first_name: Stefan full_name: Canzar, Stefan last_name: Canzar - first_name: Francisca full_name: Rojas Ringeling, Francisca last_name: Rojas Ringeling extern: '1' external_id: pmid: - '31583641' intvolume: ' 2074' language: - iso: eng month: '10' oa_version: None page: 215–231 pmid: 1 publication: Protein-Protein Interaction Networks publication_identifier: eisbn: - '9781493998739' eissn: - 1940-6029 isbn: - '9781493998722' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Vienna Graph Clustering type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2074 year: '2019' ... --- _id: '11853' abstract: - lang: eng text: We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input set system is undergoing element insertions and deletions. Here, n denotes the number of elements, each element appears in at most f sets, and the cost of each set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17], implies that there is a deterministic algorithm for this problem with O(f log(Cn)) amortized update time and O(min(log n, f)) -approximation ratio, which nearly matches the polynomial-time hardness of approximation for minimum set cover in the static setting. Our update time is only O(log (Cn)) away from a trivial lower bound. Prior to our work, the previous best approximation ratio guaranteed by deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15]. In contrast, the only result that guaranteed O(f) -approximation was obtained very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the extra O(f) factor in the update time compared to our and Gupta~et~al.'s results, the Abboud~et~al.~algorithm is randomized, and works only when the adversary is oblivious and the sets are unweighted (each set has the same cost). We achieve our result via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual algorithms that try to satisfy some local constraints for individual sets at all time, our algorithm basically waits until the dual solution changes significantly globally, and fixes the solution only where the fix is needed. article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. A new deterministic algorithm for dynamic set cover. In: 60th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2019:406-423. doi:10.1109/focs.2019.00033' apa: 'Bhattacharya, S., Henzinger, M. H., & Nanongkai, D. (2019). A new deterministic algorithm for dynamic set cover. In 60th Annual Symposium on Foundations of Computer Science (pp. 406–423). Baltimore, MD, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2019.00033' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “A New Deterministic Algorithm for Dynamic Set Cover.” In 60th Annual Symposium on Foundations of Computer Science, 406–23. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/focs.2019.00033. ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “A new deterministic algorithm for dynamic set cover,” in 60th Annual Symposium on Foundations of Computer Science, Baltimore, MD, United States, 2019, pp. 406–423. ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2019. A new deterministic algorithm for dynamic set cover. 60th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 406–423.' mla: Bhattacharya, Sayan, et al. “A New Deterministic Algorithm for Dynamic Set Cover.” 60th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2019, pp. 406–23, doi:10.1109/focs.2019.00033. short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 60th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2019, pp. 406–423. conference: end_date: 2019-11-12 location: Baltimore, MD, United States name: 'FOCS: Annual Symposium on Foundations of Computer Science' start_date: 2019-11-09 date_created: 2022-08-16T08:00:00Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-02-17T09:50:37Z day: '01' doi: 10.1109/focs.2019.00033 extern: '1' external_id: arxiv: - '1909.11600' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.11600 month: '11' oa: 1 oa_version: Preprint page: 406-423 publication: 60th Annual Symposium on Foundations of Computer Science publication_identifier: eisbn: - 978-1-7281-4952-3 isbn: - 978-1-7281-4953-0 issn: - 2575-8454 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: A new deterministic algorithm for dynamic set cover type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11851' abstract: - lang: eng text: The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weighted sum of the cut edges. In this paper, we engineer the fastest known exact algorithm for the problem. State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce the graph size such that at least one minimum cut is maintained in the contracted graph. Our algorithm achieves improvements in running time over these algorithms by a multitude of techniques. First, we use a recently developed fast and parallel inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards, we use reductions that depend on this bound to reduce the size of the graph much faster than previously possible. We use improved data structures to further lower the running time of our algorithm. Additionally, we parallelize the contraction routines of Nagamochi et al. . Overall, we arrive at a system that significantly outperforms the fastest state-of-the-art solvers for the exact minimum cut problem. article_number: '8820968' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Noe, Alexander last_name: Noe - first_name: Christian full_name: Schulz, Christian last_name: Schulz citation: ama: 'Henzinger MH, Noe A, Schulz C. Shared-memory exact minimum cuts. In: 33rd International Parallel and Distributed Processing Symposium. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/ipdps.2019.00013' apa: 'Henzinger, M. H., Noe, A., & Schulz, C. (2019). Shared-memory exact minimum cuts. In 33rd International Parallel and Distributed Processing Symposium. Rio de Janeiro, Brazil: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ipdps.2019.00013' chicago: Henzinger, Monika H, Alexander Noe, and Christian Schulz. “Shared-Memory Exact Minimum Cuts.” In 33rd International Parallel and Distributed Processing Symposium. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/ipdps.2019.00013. ieee: M. H. Henzinger, A. Noe, and C. Schulz, “Shared-memory exact minimum cuts,” in 33rd International Parallel and Distributed Processing Symposium, Rio de Janeiro, Brazil, 2019. ista: 'Henzinger MH, Noe A, Schulz C. 2019. Shared-memory exact minimum cuts. 33rd International Parallel and Distributed Processing Symposium. IPDPS: International Parallel and Distributed Processing Symposium, 8820968.' mla: Henzinger, Monika H., et al. “Shared-Memory Exact Minimum Cuts.” 33rd International Parallel and Distributed Processing Symposium, 8820968, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/ipdps.2019.00013. short: M.H. Henzinger, A. Noe, C. Schulz, in:, 33rd International Parallel and Distributed Processing Symposium, Institute of Electrical and Electronics Engineers, 2019. conference: end_date: 2019-05-24 location: Rio de Janeiro, Brazil name: 'IPDPS: International Parallel and Distributed Processing Symposium' start_date: 2019-05-20 date_created: 2022-08-16T07:25:23Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-02-21T16:30:34Z day: '01' doi: 10.1109/ipdps.2019.00013 extern: '1' external_id: arxiv: - '1808.05458' language: - iso: eng main_file_link: - url: https://arxiv.org/abs/1808.05458 month: '05' oa_version: Preprint publication: 33rd International Parallel and Distributed Processing Symposium publication_identifier: eisbn: - 978-1-7281-1246-6 eissn: - 1530-2075 isbn: - 978-1-7281-1247-3 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' related_material: record: - id: '11851' relation: later_version status: public scopus_import: '1' status: public title: Shared-memory exact minimum cuts type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11865' abstract: - lang: eng text: We present the first sublinear-time algorithm that can compute the edge connectivity λ of a network exactly on distributed message-passing networks (the CONGEST model), as long as the network contains no multi-edge. We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity λ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes Õ(n1−1/353D1/353+n1−1/706) time to compute λ and a cut of cardinality λ with high probability, where n and D are the number of nodes and the diameter of the network, respectively, and Õ hides polylogarithmic factors. This running time is sublinear in n (i.e. Õ(n1−є)) whenever D is. Previous sublinear-time distributed algorithms can solve this problem either (i) exactly only when λ=O(n1/8−є) [Thurimella PODC’95; Pritchard, Thurimella, ACM Trans. Algorithms’11; Nanongkai, Su, DISC’14] or (ii) approximately [Ghaffari, Kuhn, DISC’13; Nanongkai, Su, DISC’14]. To achieve this we develop and combine several new techniques. First, we design the first distributed algorithm that can compute a k-edge connectivity certificate for any k=O(n1−є) in time Õ(√nk+D). The previous sublinear-time algorithm can do so only when k=o(√n) [Thurimella PODC’95]. In fact, our algorithm can be turned into the first parallel algorithm with polylogarithmic depth and near-linear work. Previous near-linear work algorithms are essentially sequential and previous polylogarithmic-depth algorithms require Ω(mk) work in the worst case (e.g. [Karger, Motwani, STOC’93]). Second, we show that by combining the recent distributed expander decomposition technique of [Chang, Pettie, Zhang, SODA’19] with techniques from the sequential deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC’15], we can decompose the network into a sublinear number of clusters with small average diameter and without any mincut separating a cluster (except the “trivial” ones). This leads to a simplification of the Kawarabayashi-Thorup framework (except that we are randomized while they are deterministic). This might make this framework more useful in other models of computation. Finally, by extending the tree packing technique from [Karger STOC’96], we can find the minimum cut in time proportional to the number of components. As a byproduct of this technique, we obtain an Õ(n)-time algorithm for computing exact minimum cut for weighted graphs. article_processing_charge: No author: - first_name: Mohit full_name: Daga, Mohit last_name: Daga - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai - first_name: Thatchaphol full_name: Saranurak, Thatchaphol last_name: Saranurak citation: ama: 'Daga M, Henzinger MH, Nanongkai D, Saranurak T. Distributed edge connectivity in sublinear time. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. Association for Computing Machinery; 2019:343–354. doi:10.1145/3313276.3316346' apa: 'Daga, M., Henzinger, M. H., Nanongkai, D., & Saranurak, T. (2019). Distributed edge connectivity in sublinear time. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 343–354). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3313276.3316346' chicago: Daga, Mohit, Monika H Henzinger, Danupon Nanongkai, and Thatchaphol Saranurak. “Distributed Edge Connectivity in Sublinear Time.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 343–354. Association for Computing Machinery, 2019. https://doi.org/10.1145/3313276.3316346. ieee: M. Daga, M. H. Henzinger, D. Nanongkai, and T. Saranurak, “Distributed edge connectivity in sublinear time,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 343–354. ista: 'Daga M, Henzinger MH, Nanongkai D, Saranurak T. 2019. Distributed edge connectivity in sublinear time. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 343–354.' mla: Daga, Mohit, et al. “Distributed Edge Connectivity in Sublinear Time.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2019, pp. 343–354, doi:10.1145/3313276.3316346. short: M. Daga, M.H. Henzinger, D. Nanongkai, T. Saranurak, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing Machinery, 2019, pp. 343–354. conference: end_date: 2019-06-26 location: Phoenix, AZ, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2019-06-23 date_created: 2022-08-16T09:11:17Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-02-17T10:26:25Z day: '01' doi: 10.1145/3313276.3316346 extern: '1' external_id: arxiv: - '1904.04341' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.04341 month: '06' oa: 1 oa_version: Preprint page: 343–354 publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing publication_identifier: isbn: - 978-1-4503-6705-9 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Distributed edge connectivity in sublinear time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11871' abstract: - lang: eng text: "Many dynamic graph algorithms have an amortized update time, rather than a stronger worst-case guarantee. But amortized data structures are not suitable for real-time systems, where each individual operation has to be executed quickly. For this reason, there exist many recent randomized results that aim to provide a guarantee stronger than amortized expected. The strongest possible guarantee for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability worst-case update time, which gives a bound on the time for each individual operation that holds with high probability.\r\n\r\nIn this paper we present the first polylogarithmic high-probability worst-case time bounds for the dynamic spanner and the dynamic maximal matching problem.\r\n\r\n1.\t\r\nFor dynamic spanner, the only known o(n) worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n) high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which yields the first worst-case polylog update time for all constant k. (All the results above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.)\r\n\r\n2.\t\r\nFor dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm with o(n) worst-case time bound was known and we present an algorithm with O(log5 (n)) high-probability worst-case time; similar worst-case bounds existed only for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal.\r\n\r\nOur results are achieved using a new approach for converting amortized guarantees to worst-case ones for randomized data structures by going through a third type of guarantee, which is a middle ground between the two above: an algorithm is said to have worst-case expected update time α if for every update σ, the expected time to process σ is at most α. Although stronger than amortized expected, the worst-case expected guarantee does not resolve the fundamental problem of amortization: a worst-case expected update time of O(1) still allows for the possibility that every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n). In this paper we present a black-box reduction that converts any data structure with worst-case expected update time into one with a high-probability worst-case update time: the query time remains the same, while the update time increases by a factor of O(log2(n)).\r\n\r\nThus we achieve our results in two steps: (1) First we show how to convert existing dynamic graph algorithms with amortized expected polylogarithmic running times into algorithms with worst-case expected polylogarithmic running times. (2) Then we use our black-box reduction to achieve the polylogarithmic high-probability worst-case time bound. All our algorithms are Las-Vegas-type algorithms." article_processing_charge: No author: - first_name: Aaron full_name: Bernstein, Aaron last_name: Bernstein - first_name: Sebastian full_name: Forster, Sebastian last_name: Forster - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 citation: ama: 'Bernstein A, Forster S, Henzinger MH. A deamortization approach for dynamic spanner and dynamic maximal matching. In: 30th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2019:1899-1918. doi:10.1137/1.9781611975482.115' apa: 'Bernstein, A., Forster, S., & Henzinger, M. H. (2019). A deamortization approach for dynamic spanner and dynamic maximal matching. In 30th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1899–1918). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975482.115' chicago: Bernstein, Aaron, Sebastian Forster, and Monika H Henzinger. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” In 30th Annual ACM-SIAM Symposium on Discrete Algorithms, 1899–1918. Society for Industrial and Applied Mathematics, 2019. https://doi.org/10.1137/1.9781611975482.115. ieee: A. Bernstein, S. Forster, and M. H. Henzinger, “A deamortization approach for dynamic spanner and dynamic maximal matching,” in 30th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2019, pp. 1899–1918. ista: 'Bernstein A, Forster S, Henzinger MH. 2019. A deamortization approach for dynamic spanner and dynamic maximal matching. 30th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1899–1918.' mla: Bernstein, Aaron, et al. “A Deamortization Approach for Dynamic Spanner and Dynamic Maximal Matching.” 30th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019, pp. 1899–918, doi:10.1137/1.9781611975482.115. short: A. Bernstein, S. Forster, M.H. Henzinger, in:, 30th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019, pp. 1899–1918. conference: end_date: 2019-01-09 location: San Diego, CA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2019-01-06 date_created: 2022-08-16T09:50:33Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-02-21T16:31:21Z day: '01' doi: 10.1137/1.9781611975482.115 extern: '1' external_id: arxiv: - '1810.10932' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.10932 month: '01' oa: 1 oa_version: Preprint page: 1899-1918 publication: 30th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-1-61197-548-2 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '11871' relation: earlier_version status: public scopus_import: '1' status: public title: A deamortization approach for dynamic spanner and dynamic maximal matching type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '11898' abstract: - lang: eng text: "We build upon the recent papers by Weinstein and Yu (FOCS'16), Larsen (FOCS'12), and Clifford et al. (FOCS'15) to present a general framework that gives amortized lower bounds on the update and query times of dynamic data structures. Using our framework, we present two concrete results.\r\n(1) For the dynamic polynomial evaluation problem, where the polynomial is defined over a finite field of size n1+Ω(1) and has degree n, any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω((lgn/lglgn)2).\r\n(2) For the dynamic online matrix vector multiplication problem, where we get an n×n matrix whose entires are drawn from a finite field of size nΘ(1), any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω(n⋅(lgn/lglgn)2).\r\nFor these two problems, the previous works by Larsen (FOCS'12) and Clifford et al. (FOCS'15) gave the same lower bounds, but only for worst case update and query times. Our bounds match the highest unconditional lower bounds known till date for any dynamic problem in the cell-probe model." article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Stefan full_name: Neumann, Stefan last_name: Neumann citation: ama: Bhattacharya S, Henzinger MH, Neumann S. New amortized cell-probe lower bounds for dynamic problems. Theoretical Computer Science. 2019;779:72-87. doi:10.1016/j.tcs.2019.01.043 apa: Bhattacharya, S., Henzinger, M. H., & Neumann, S. (2019). New amortized cell-probe lower bounds for dynamic problems. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2019.01.043 chicago: Bhattacharya, Sayan, Monika H Henzinger, and Stefan Neumann. “New Amortized Cell-Probe Lower Bounds for Dynamic Problems.” Theoretical Computer Science. Elsevier, 2019. https://doi.org/10.1016/j.tcs.2019.01.043. ieee: S. Bhattacharya, M. H. Henzinger, and S. Neumann, “New amortized cell-probe lower bounds for dynamic problems,” Theoretical Computer Science, vol. 779. Elsevier, pp. 72–87, 2019. ista: Bhattacharya S, Henzinger MH, Neumann S. 2019. New amortized cell-probe lower bounds for dynamic problems. Theoretical Computer Science. 779, 72–87. mla: Bhattacharya, Sayan, et al. “New Amortized Cell-Probe Lower Bounds for Dynamic Problems.” Theoretical Computer Science, vol. 779, Elsevier, 2019, pp. 72–87, doi:10.1016/j.tcs.2019.01.043. short: S. Bhattacharya, M.H. Henzinger, S. Neumann, Theoretical Computer Science 779 (2019) 72–87. date_created: 2022-08-17T09:02:15Z date_published: 2019-08-02T00:00:00Z date_updated: 2022-09-09T11:29:04Z day: '02' doi: 10.1016/j.tcs.2019.01.043 extern: '1' external_id: arxiv: - '1902.02304' intvolume: ' 779' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.02304 month: '08' oa: 1 oa_version: Preprint page: 72-87 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: New amortized cell-probe lower bounds for dynamic problems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 779 year: '2019' ... --- _id: '11957' abstract: - lang: eng text: Cross-coupling reactions mediated by dual nickel/photocatalysis are synthetically attractive but rely mainly on expensive, non-recyclable noble-metal complexes as photocatalysts. Heterogeneous semiconductors, which are commonly used for artificial photosynthesis and wastewater treatment, are a sustainable alternative. Graphitic carbon nitrides, a class of metal-free polymers that can be easily prepared from bulk chemicals, are heterogeneous semiconductors with high potential for photocatalytic organic transformations. Here, we demonstrate that graphitic carbon nitrides in combination with nickel catalysis can induce selective C−O cross-couplings of carboxylic acids with aryl halides, yielding the respective aryl esters in excellent yield and selectivity. The heterogeneous organic photocatalyst exhibits a broad substrate scope, is able to harvest green light, and can be recycled multiple times. In situ FTIR was used to track the reaction progress to study this transformation at different irradiation wavelengths and reaction scales. article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Jamal A. full_name: Malik, Jamal A. last_name: Malik - first_name: Cristian full_name: Cavedon, Cristian last_name: Cavedon - first_name: Sebastian full_name: Gisbertz, Sebastian last_name: Gisbertz - first_name: Aleksandr full_name: Savateev, Aleksandr last_name: Savateev - first_name: Daniel full_name: Cruz, Daniel last_name: Cruz - first_name: Tobias full_name: Heil, Tobias last_name: Heil - first_name: Guigang full_name: Zhang, Guigang last_name: Zhang - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger citation: ama: 'Pieber B, Malik JA, Cavedon C, et al. Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides. Angewandte Chemie International Edition. 2019;58(28):9575-9580. doi:10.1002/anie.201902785' apa: 'Pieber, B., Malik, J. A., Cavedon, C., Gisbertz, S., Savateev, A., Cruz, D., … Seeberger, P. H. (2019). Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201902785' chicago: 'Pieber, Bartholomäus, Jamal A. Malik, Cristian Cavedon, Sebastian Gisbertz, Aleksandr Savateev, Daniel Cruz, Tobias Heil, Guigang Zhang, and Peter H. Seeberger. “Semi‐heterogeneous Dual Nickel/Photocatalysis Using Carbon Nitrides: Esterification of Carboxylic Acids with Aryl Halides.” Angewandte Chemie International Edition. Wiley, 2019. https://doi.org/10.1002/anie.201902785.' ieee: 'B. Pieber et al., “Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides,” Angewandte Chemie International Edition, vol. 58, no. 28. Wiley, pp. 9575–9580, 2019.' ista: 'Pieber B, Malik JA, Cavedon C, Gisbertz S, Savateev A, Cruz D, Heil T, Zhang G, Seeberger PH. 2019. Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides. Angewandte Chemie International Edition. 58(28), 9575–9580.' mla: 'Pieber, Bartholomäus, et al. “Semi‐heterogeneous Dual Nickel/Photocatalysis Using Carbon Nitrides: Esterification of Carboxylic Acids with Aryl Halides.” Angewandte Chemie International Edition, vol. 58, no. 28, Wiley, 2019, pp. 9575–80, doi:10.1002/anie.201902785.' short: B. Pieber, J.A. Malik, C. Cavedon, S. Gisbertz, A. Savateev, D. Cruz, T. Heil, G. Zhang, P.H. Seeberger, Angewandte Chemie International Edition 58 (2019) 9575–9580. date_created: 2022-08-24T10:50:19Z date_published: 2019-07-08T00:00:00Z date_updated: 2023-02-21T10:09:16Z day: '08' doi: 10.1002/anie.201902785 extern: '1' external_id: pmid: - '31050132' intvolume: ' 58' issue: '28' language: - iso: eng month: '07' oa_version: None page: 9575-9580 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Semi‐heterogeneous dual nickel/photocatalysis using carbon nitrides: Esterification of carboxylic acids with aryl halides' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2019' ... --- _id: '11984' abstract: - lang: eng text: Differentially protected galactosamine building blocks are key components for the synthesis of human and bacterial oligosaccharides. The azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal provides straightforward access to the corresponding 2-nitrogenated glycoside. Poor reproducibility and the use of azides that lead to the formation of potentially explosive and toxic species limit the scalability of this reaction and render it a bottleneck for carbohydrate synthesis. Here, we present a method for the safe, efficient, and reliable azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal at room temperature, using continuous flow chemistry. Careful analysis of the transformation resulted in reaction conditions that produce minimal side products while the reaction time was reduced drastically when compared to batch reactions. The flow setup is readily scalable to process 5 mmol of galactal in 3 h, producing 1.2 mmol/h of product. article_processing_charge: No article_type: letter_note author: - first_name: Mónica full_name: Guberman, Mónica last_name: Guberman - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger citation: ama: Guberman M, Pieber B, Seeberger PH. Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. Organic Process Research and Development. 2019;23(12):2764-2770. doi:10.1021/acs.oprd.9b00456 apa: Guberman, M., Pieber, B., & Seeberger, P. H. (2019). Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. Organic Process Research and Development. American Chemical Society. https://doi.org/10.1021/acs.oprd.9b00456 chicago: Guberman, Mónica, Bartholomäus Pieber, and Peter H. Seeberger. “Safe and Scalable Continuous Flow Azidophenylselenylation of Galactal to Prepare Galactosamine Building Blocks.” Organic Process Research and Development. American Chemical Society, 2019. https://doi.org/10.1021/acs.oprd.9b00456. ieee: M. Guberman, B. Pieber, and P. H. Seeberger, “Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks,” Organic Process Research and Development, vol. 23, no. 12. American Chemical Society, pp. 2764–2770, 2019. ista: Guberman M, Pieber B, Seeberger PH. 2019. Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks. Organic Process Research and Development. 23(12), 2764–2770. mla: Guberman, Mónica, et al. “Safe and Scalable Continuous Flow Azidophenylselenylation of Galactal to Prepare Galactosamine Building Blocks.” Organic Process Research and Development, vol. 23, no. 12, American Chemical Society, 2019, pp. 2764–70, doi:10.1021/acs.oprd.9b00456. short: M. Guberman, B. Pieber, P.H. Seeberger, Organic Process Research and Development 23 (2019) 2764–2770. date_created: 2022-08-25T11:30:33Z date_published: 2019-12-20T00:00:00Z date_updated: 2023-02-21T10:10:23Z day: '20' doi: 10.1021/acs.oprd.9b00456 extern: '1' intvolume: ' 23' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acs.oprd.9b00456 month: '12' oa: 1 oa_version: Published Version page: 2764-2770 publication: Organic Process Research and Development publication_identifier: eissn: - 1520-586X issn: - 1083-6160 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2019' ... --- _id: '11982' abstract: - lang: eng text: A carbon nitride material can be combined with homogeneous nickel catalysts for light-mediated cross-couplings of aryl bromides with alcohols under mild conditions. The metal-free heterogeneous semiconductor is fully recyclable and couples a broad range of electron-poor aryl bromides with primary and secondary alcohols as well as water. The application for intramolecular reactions and the synthesis of active pharmaceutical ingredients was demonstrated. The catalytic protocol is applicable for the coupling of aryl iodides with thiols as well. article_processing_charge: No article_type: letter_note author: - first_name: Cristian full_name: Cavedon, Cristian last_name: Cavedon - first_name: Amiera full_name: Madani, Amiera last_name: Madani - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X citation: ama: Cavedon C, Madani A, Seeberger PH, Pieber B. Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides. Organic Letters. 2019;21(13):5331-5334. doi:10.1021/acs.orglett.9b01957 apa: Cavedon, C., Madani, A., Seeberger, P. H., & Pieber, B. (2019). Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides. Organic Letters. American Chemical Society. https://doi.org/10.1021/acs.orglett.9b01957 chicago: Cavedon, Cristian, Amiera Madani, Peter H. Seeberger, and Bartholomäus Pieber. “Semiheterogeneous Dual Nickel/Photocatalytic (Thio)Etherification Using Carbon Nitrides.” Organic Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.orglett.9b01957. ieee: C. Cavedon, A. Madani, P. H. Seeberger, and B. Pieber, “Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides,” Organic Letters, vol. 21, no. 13. American Chemical Society, pp. 5331–5334, 2019. ista: Cavedon C, Madani A, Seeberger PH, Pieber B. 2019. Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides. Organic Letters. 21(13), 5331–5334. mla: Cavedon, Cristian, et al. “Semiheterogeneous Dual Nickel/Photocatalytic (Thio)Etherification Using Carbon Nitrides.” Organic Letters, vol. 21, no. 13, American Chemical Society, 2019, pp. 5331–34, doi:10.1021/acs.orglett.9b01957. short: C. Cavedon, A. Madani, P.H. Seeberger, B. Pieber, Organic Letters 21 (2019) 5331–5334. date_created: 2022-08-25T11:18:00Z date_published: 2019-07-05T00:00:00Z date_updated: 2023-02-21T10:10:19Z day: '05' doi: 10.1021/acs.orglett.9b01957 extern: '1' external_id: pmid: - '31247752' intvolume: ' 21' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acs.orglett.9b01957 month: '07' oa: 1 oa_version: Published Version page: 5331-5334 pmid: 1 publication: Organic Letters publication_identifier: eissn: - 1523-7052 issn: - 1523-7060 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2019' ... --- _id: '170' abstract: - lang: eng text: Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ . author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Efthymios full_name: Sofos, Efthymios last_name: Sofos citation: ama: Browning TD, Sofos E. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 2019;373(3-4):977-1016. doi:10.1007/s00208-018-1716-6 apa: Browning, T. D., & Sofos, E. (2019). Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-018-1716-6 chicago: Browning, Timothy D, and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen. Springer Nature, 2019. https://doi.org/10.1007/s00208-018-1716-6. ieee: T. D. Browning and E. Sofos, “Counting rational points on quartic del Pezzo surfaces with a rational conic,” Mathematische Annalen, vol. 373, no. 3–4. Springer Nature, pp. 977–1016, 2019. ista: Browning TD, Sofos E. 2019. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 373(3–4), 977–1016. mla: Browning, Timothy D., and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen, vol. 373, no. 3–4, Springer Nature, 2019, pp. 977–1016, doi:10.1007/s00208-018-1716-6. short: T.D. Browning, E. Sofos, Mathematische Annalen 373 (2019) 977–1016. date_created: 2018-12-11T11:44:59Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '01' ddc: - '510' doi: 10.1007/s00208-018-1716-6 extern: '1' external_id: arxiv: - '1609.09057' file: - access_level: open_access checksum: 4061dc2fe99bee25d9adf2d2018cf608 content_type: application/pdf creator: dernst date_created: 2019-05-23T07:53:27Z date_updated: 2020-07-14T12:45:12Z file_id: '6479' file_name: 2019_MathAnnalen_Browning.pdf file_size: 712847 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 373' issue: 3-4 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '04' oa: 1 oa_version: Published Version page: 977-1016 publication: Mathematische Annalen publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Counting rational points on quartic del Pezzo surfaces with a rational conic tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 373 year: '2019' ... --- _id: '441' article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X citation: ama: Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0 apa: Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0 chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40879-018-0218-0. ieee: N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019. ista: Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928. mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0. short: N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928. date_created: 2018-12-11T11:46:29Z date_published: 2019-09-15T00:00:00Z date_updated: 2021-01-12T07:56:46Z day: '15' department: - _id: TaHa doi: 10.1007/s40879-018-0218-0 ec_funded: 1 external_id: arxiv: - '1711.02089' intvolume: ' 5' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.02089 month: '09' oa: 1 oa_version: Preprint page: 909–928 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: European Journal of Mathematics publication_identifier: eissn: - 2199-6768 issn: - 2199-675X publication_status: published publisher: Springer Nature publist_id: '7382' quality_controlled: '1' scopus_import: 1 status: public title: Tropical formulae for summation over a part of SL(2,Z) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 5 year: '2019' ... --- _id: '5793' abstract: - lang: eng text: The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis. alternative_title: - MIMB author: - first_name: Yoichi full_name: Asaoka, Yoichi last_name: Asaoka - first_name: Hitoshi full_name: Morita, Hitoshi last_name: Morita - first_name: Hiroko full_name: Furumoto, Hiroko last_name: Furumoto - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Makoto full_name: Furutani-Seiki, Makoto last_name: Furutani-Seiki citation: ama: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14' apa: Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14 chicago: Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14. ieee: Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181. ista: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.' mla: Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14. short: Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181. date_created: 2019-01-06T22:59:11Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:03:30Z day: '01' department: - _id: CaHe doi: 10.1007/978-1-4939-8910-2_14 editor: - first_name: Alexander full_name: Hergovich, Alexander last_name: Hergovich intvolume: ' 1893' language: - iso: eng month: '01' oa_version: None page: 167-181 publication: The hippo pathway publication_identifier: isbn: - 978-1-4939-8909-6 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: 1 series_title: Methods in Molecular Biology status: public title: Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1893 year: '2019' ... --- _id: '5887' abstract: - lang: eng text: 'Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.' article_processing_charge: No article_type: original author: - first_name: Gregory full_name: Demay, Gregory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Bjorn full_name: Tackmann, Bjorn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 2019;27(1):75-111. doi:10.3233/JCS-181131' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2019). Per-session security: Password-based cryptography revisited. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-181131' chicago: 'Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security. IOS Press, 2019. https://doi.org/10.3233/JCS-181131.' ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based cryptography revisited,” Journal of Computer Security, vol. 27, no. 1. IOS Press, pp. 75–111, 2019.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based cryptography revisited. Journal of Computer Security. 27(1), 75–111.' mla: 'Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography Revisited.” Journal of Computer Security, vol. 27, no. 1, IOS Press, 2019, pp. 75–111, doi:10.3233/JCS-181131.' short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27 (2019) 75–111. date_created: 2019-01-27T22:59:10Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:05:08Z day: '1' department: - _id: KrPi doi: 10.3233/JCS-181131 ec_funded: 1 intvolume: ' 27' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/166 month: '01' oa: 1 oa_version: Preprint page: 75-111 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Journal of Computer Security publication_identifier: issn: - 0926227X publication_status: published publisher: IOS Press quality_controlled: '1' scopus_import: '1' status: public title: 'Per-session security: Password-based cryptography revisited' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2019' ... --- _id: '6163' abstract: - lang: eng text: We propose a new non-orthogonal basis to express the 3D Euclidean space in terms of a regular grid. Every grid point, each represented by integer 3-coordinates, corresponds to rhombic dodecahedron centroid. Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. A characterization of a 3D digital sphere with relevant topological features is proposed as well with the help of a 48 symmetry that comes with the new coordinate system. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Gaëlle full_name: Largeteau-Skapin, Gaëlle last_name: Largeteau-Skapin - first_name: Rita full_name: Zrour, Rita last_name: Zrour - first_name: Eric full_name: Andres, Eric last_name: Andres citation: ama: 'Biswas R, Largeteau-Skapin G, Zrour R, Andres E. Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. In: 21st IAPR International Conference on Discrete Geometry for Computer Imagery. Vol 11414. Berlin, Heidelberg: Springer Berlin Heidelberg; 2019:27-37. doi:10.1007/978-3-030-14085-4_3' apa: 'Biswas, R., Largeteau-Skapin, G., Zrour, R., & Andres, E. (2019). Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. In 21st IAPR International Conference on Discrete Geometry for Computer Imagery (Vol. 11414, pp. 27–37). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-030-14085-4_3' chicago: 'Biswas, Ranita, Gaëlle Largeteau-Skapin, Rita Zrour, and Eric Andres. “Rhombic Dodecahedron Grid—Coordinate System and 3D Digital Object Definitions.” In 21st IAPR International Conference on Discrete Geometry for Computer Imagery, 11414:27–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. https://doi.org/10.1007/978-3-030-14085-4_3.' ieee: R. Biswas, G. Largeteau-Skapin, R. Zrour, and E. Andres, “Rhombic dodecahedron grid—coordinate system and 3D digital object definitions,” in 21st IAPR International Conference on Discrete Geometry for Computer Imagery, Marne-la-Vallée, France, 2019, vol. 11414, pp. 27–37. ista: 'Biswas R, Largeteau-Skapin G, Zrour R, Andres E. 2019. Rhombic dodecahedron grid—coordinate system and 3D digital object definitions. 21st IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 11414, 27–37.' mla: Biswas, Ranita, et al. “Rhombic Dodecahedron Grid—Coordinate System and 3D Digital Object Definitions.” 21st IAPR International Conference on Discrete Geometry for Computer Imagery, vol. 11414, Springer Berlin Heidelberg, 2019, pp. 27–37, doi:10.1007/978-3-030-14085-4_3. short: R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, in:, 21st IAPR International Conference on Discrete Geometry for Computer Imagery, Springer Berlin Heidelberg, Berlin, Heidelberg, 2019, pp. 27–37. conference: end_date: 2019-03-28 location: Marne-la-Vallée, France name: 'DGCI: International Conference on Discrete Geometry for Computer Imagery' start_date: 2019-03-26 date_created: 2019-03-21T12:12:19Z date_published: 2019-02-23T00:00:00Z date_updated: 2022-01-27T14:25:17Z day: '23' doi: 10.1007/978-3-030-14085-4_3 extern: '1' intvolume: ' 11414' language: - iso: eng month: '02' oa_version: None page: 27-37 place: Berlin, Heidelberg publication: 21st IAPR International Conference on Discrete Geometry for Computer Imagery publication_identifier: isbn: - 978-3-6624-6446-5 - 978-3-6624-6447-2 issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Berlin Heidelberg quality_controlled: '1' status: public title: Rhombic dodecahedron grid—coordinate system and 3D digital object definitions type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11414 year: '2019' ... --- _id: '6515' abstract: - lang: eng text: We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature. author: - first_name: Ramsay full_name: Dyer, Ramsay last_name: Dyer - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 2019;10(1):223–256. doi:10.20382/jocg.v10i1a9 apa: Dyer, R., Vegter, G., & Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . Carleton University. https://doi.org/10.20382/jocg.v10i1a9 chicago: Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry . Carleton University, 2019. https://doi.org/10.20382/jocg.v10i1a9. ieee: R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” Journal of Computational Geometry , vol. 10, no. 1. Carleton University, pp. 223–256, 2019. ista: Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256. mla: Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” Journal of Computational Geometry , vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:10.20382/jocg.v10i1a9. short: R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10 (2019) 223–256. date_created: 2019-06-03T09:35:33Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:07:50Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.20382/jocg.v10i1a9 ec_funded: 1 file: - access_level: open_access checksum: 57b4df2f16a74eb499734ec8ee240178 content_type: application/pdf creator: mwintrae date_created: 2019-06-03T09:30:01Z date_updated: 2020-07-14T12:47:32Z file_id: '6516' file_name: mainJournalFinal.pdf file_size: 2170882 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 10' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 223–256 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 'Journal of Computational Geometry ' publication_identifier: issn: - 1920-180X publication_status: published publisher: Carleton University quality_controlled: '1' scopus_import: 1 status: public title: Simplices modelled on spaces of constant curvature tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '6528' abstract: - lang: eng text: We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism. alternative_title: - LIPIcs article_number: '60' article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Simple verifiable delay functions. In: 10th Innovations in Theoretical Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.ITCS.2019.60' apa: 'Pietrzak, K. Z. (2019). Simple verifiable delay functions. In 10th Innovations in Theoretical Computer Science Conference (Vol. 124). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.60' chicago: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In 10th Innovations in Theoretical Computer Science Conference, Vol. 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ITCS.2019.60. ieee: K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations in Theoretical Computer Science Conference, San Diego, CA, United States, 2019, vol. 124. ista: 'Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in Theoretical Computer Science Conference. ITCS 2019: Innovations in Theoretical Computer Science, LIPIcs, vol. 124, 60.' mla: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” 10th Innovations in Theoretical Computer Science Conference, vol. 124, 60, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ITCS.2019.60. short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-01-12 location: San Diego, CA, United States name: 'ITCS 2019: Innovations in Theoretical Computer Science' start_date: 2019-01-10 date_created: 2019-06-06T14:12:36Z date_published: 2019-01-10T00:00:00Z date_updated: 2021-01-12T08:07:53Z day: '10' ddc: - '000' department: - _id: KrPi doi: 10.4230/LIPICS.ITCS.2019.60 ec_funded: 1 file: - access_level: open_access checksum: f0ae1bb161431d9db3dea5ace082bfb5 content_type: application/pdf creator: dernst date_created: 2019-06-06T14:22:04Z date_updated: 2020-07-14T12:47:33Z file_id: '6529' file_name: 2019_LIPIcs_Pietrzak.pdf file_size: 558770 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 124' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/627 month: '01' oa: 1 oa_version: Published Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 10th Innovations in Theoretical Computer Science Conference publication_identifier: isbn: - 978-3-95977-095-8 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Simple verifiable delay functions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2019' ... --- _id: '6565' abstract: - lang: eng text: In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example. article_number: '8715598' article_processing_charge: No author: - first_name: Atreyee full_name: Kundu, Atreyee last_name: Kundu - first_name: Miriam full_name: Garcia Soto, Miriam id: 4B3207F6-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Soto orcid: 0000−0003−2936−5719 - first_name: Pavithra full_name: Prabhakar, Pavithra last_name: Prabhakar citation: ama: 'Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In: 5th Indian Control Conference Proceedings. IEEE; 2019. doi:10.1109/INDIANCC.2019.8715598' apa: 'Kundu, A., Garcia Soto, M., & Prabhakar, P. (2019). Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. In 5th Indian Control Conference Proceedings. Delhi, India: IEEE. https://doi.org/10.1109/INDIANCC.2019.8715598' chicago: Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” In 5th Indian Control Conference Proceedings. IEEE, 2019. https://doi.org/10.1109/INDIANCC.2019.8715598. ieee: A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing controllers for periodically controlled linear switched systems,” in 5th Indian Control Conference Proceedings, Delhi, India, 2019. ista: Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing controllers for periodically controlled linear switched systems. 5th Indian Control Conference Proceedings. ICC 2019 - Indian Control Conference, 8715598. mla: Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.” 5th Indian Control Conference Proceedings, 8715598, IEEE, 2019, doi:10.1109/INDIANCC.2019.8715598. short: A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference Proceedings, IEEE, 2019. conference: end_date: 2019-01-11 location: Delhi, India name: ICC 2019 - Indian Control Conference start_date: 2019-01-09 date_created: 2019-06-17T06:57:33Z date_published: 2019-05-16T00:00:00Z date_updated: 2021-01-12T08:08:01Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1109/INDIANCC.2019.8715598 file: - access_level: open_access checksum: d622a91af1e427f6b1e0ba8e18a2b767 content_type: application/pdf creator: dernst date_created: 2020-10-21T13:13:49Z date_updated: 2020-10-21T13:13:49Z file_id: '8687' file_name: 2019_ICC_Kundu.pdf file_size: 396031 relation: main_file success: 1 file_date_updated: 2020-10-21T13:13:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 5th Indian Control Conference Proceedings publication_identifier: isbn: - 978-153866246-5 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Formal synthesis of stabilizing controllers for periodically controlled linear switched systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6628' abstract: - lang: eng text: Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space. author: - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: 'Vegter G, Wintraecken M. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In: The 31st Canadian Conference in Computational Geometry. ; 2019:275-279.' apa: Vegter, G., & Wintraecken, M. (2019). The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. In The 31st Canadian Conference in Computational Geometry (pp. 275–279). Edmonton, Canada. chicago: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” In The 31st Canadian Conference in Computational Geometry, 275–79, 2019. ieee: G. Vegter and M. Wintraecken, “The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds,” in The 31st Canadian Conference in Computational Geometry, Edmonton, Canada, 2019, pp. 275–279. ista: 'Vegter G, Wintraecken M. 2019. The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds. The 31st Canadian Conference in Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 275–279.' mla: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff Distance of Optimal Triangulations of Manifolds.” The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–79. short: G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational Geometry, 2019, pp. 275–279. conference: end_date: 2019-08-10 location: Edmonton, Canada name: 'CCCG: Canadian Conference in Computational Geometry' start_date: 2019-08-08 date_created: 2019-07-12T08:34:57Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:08:16Z day: '01' ddc: - '004' department: - _id: HeEd ec_funded: 1 file: - access_level: open_access checksum: ceabd152cfa55170d57763f9c6c60a53 content_type: application/pdf creator: mwintrae date_created: 2019-07-12T08:32:46Z date_updated: 2020-07-14T12:47:34Z file_id: '6629' file_name: IntrinsicExtrinsicCCCG2019.pdf file_size: 321176 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 275-279 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: The 31st Canadian Conference in Computational Geometry publication_status: published quality_controlled: '1' scopus_import: 1 status: public title: The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '6648' abstract: - lang: eng text: "Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory\r\nneeded for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context." alternative_title: - LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ziga full_name: Virk, Ziga last_name: Virk - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31' apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis in information space. In 35th International Symposium on Computational Geometry (Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31' chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” In 35th International Symposium on Computational Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31. ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 31:1-31:14. ista: 'Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.' mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31. short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG 2019: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2019-07-17T10:36:09Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:08:23Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.4230/LIPICS.SOCG.2019.31 external_id: arxiv: - '1903.08510' file: - access_level: open_access checksum: 8ec8720730d4c789bf7b06540f1c29f4 content_type: application/pdf creator: dernst date_created: 2019-07-24T06:40:01Z date_updated: 2020-07-14T12:47:35Z file_id: '6666' file_name: 2019_LIPICS_Edelsbrunner.pdf file_size: 1355179 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 31:1-31:14 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: 35th International Symposium on Computational Geometry publication_identifier: isbn: - '9783959771047' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Topological data analysis in information space tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '6659' abstract: - lang: eng text: Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research. acknowledgement: his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation. article_processing_charge: No article_type: original author: - first_name: Naoki full_name: Zenmyo, Naoki last_name: Zenmyo - first_name: Hiroki full_name: Tokumaru, Hiroki last_name: Tokumaru - first_name: Shohei full_name: Uchinomiya, Shohei last_name: Uchinomiya - first_name: Hirokazu full_name: Fuchida, Hirokazu last_name: Fuchida - first_name: Shigekazu full_name: Tabata, Shigekazu id: 4427179E-F248-11E8-B48F-1D18A9856A87 last_name: Tabata - first_name: Itaru full_name: Hamachi, Itaru last_name: Hamachi - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Akio full_name: Ojida, Akio last_name: Ojida citation: ama: Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034 apa: Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan. https://doi.org/10.1246/bcsj.20190034 chicago: Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034. ieee: N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” Bulletin of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019. ista: Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000. mla: Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034. short: N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000. date_created: 2019-07-21T21:59:16Z date_published: 2019-05-15T00:00:00Z date_updated: 2021-01-12T08:08:26Z day: '15' ddc: - '570' department: - _id: RySh doi: 10.1246/bcsj.20190034 ec_funded: 1 file: - access_level: open_access checksum: 186de511d6e0ca93f5d981e2443eb8cd content_type: application/pdf creator: dernst date_created: 2020-10-02T08:49:58Z date_updated: 2020-10-02T08:49:58Z file_id: '8594' file_name: 2019_BCSJ_Zenmyo.pdf file_size: 2464903 relation: main_file success: 1 file_date_updated: 2020-10-02T08:49:58Z has_accepted_license: '1' intvolume: ' 92' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 995-1000 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: Bulletin of the Chemical Society of Japan publication_identifier: issn: - '00092673' publication_status: published publisher: Bulletin of the Chemical Society of Japan quality_controlled: '1' scopus_import: '1' status: public title: Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2019' ... --- _id: '6662' abstract: - lang: eng text: "In phase retrieval, we want to recover an unknown signal \U0001D465∈ℂ\U0001D451 from n quadratic measurements of the form \U0001D466\U0001D456=|⟨\U0001D44E\U0001D456,\U0001D465⟩|2+\U0001D464\U0001D456, where \U0001D44E\U0001D456∈ℂ\U0001D451 are known sensing vectors and \U0001D464\U0001D456 is measurement noise. We ask the following weak recovery question: What is the minimum number of measurements n needed to produce an estimator \U0001D465^(\U0001D466) that is positively correlated with the signal \U0001D465? We consider the case of Gaussian vectors \U0001D44E\U0001D44E\U0001D456. We prove that—in the high-dimensional limit—a sharp phase transition takes place, and we locate the threshold in the regime of vanishingly small noise. For \U0001D45B≤\U0001D451−\U0001D45C(\U0001D451), no estimator can do significantly better than random and achieve a strictly positive correlation. For \U0001D45B≥\U0001D451+\U0001D45C(\U0001D451), a simple spectral estimator achieves a positive correlation. Surprisingly, numerical simulations with the same spectral estimator demonstrate promising performance with realistic sensing matrices. Spectral methods are used to initialize non-convex optimization algorithms in phase retrieval, and our approach can boost the performance in this setting as well. Our impossibility result is based on classical information-theoretic arguments. The spectral algorithm computes the leading eigenvector of a weighted empirical covariance matrix. We obtain a sharp characterization of the spectral properties of this random matrix using tools from free probability and generalizing a recent result by Lu and Li. Both the upper bound and lower bound generalize beyond phase retrieval to measurements \U0001D466\U0001D456 produced according to a generalized linear model. As a by-product of our analysis, we compare the threshold of the proposed spectral method with that of a message passing algorithm." article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Andrea full_name: Montanari, Andrea last_name: Montanari citation: ama: Mondelli M, Montanari A. Fundamental limits of weak recovery with applications to phase retrieval. Foundations of Computational Mathematics. 2019;19(3):703-773. doi:10.1007/s10208-018-9395-y apa: Mondelli, M., & Montanari, A. (2019). Fundamental limits of weak recovery with applications to phase retrieval. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-018-9395-y chicago: Mondelli, Marco, and Andrea Montanari. “Fundamental Limits of Weak Recovery with Applications to Phase Retrieval.” Foundations of Computational Mathematics. Springer, 2019. https://doi.org/10.1007/s10208-018-9395-y. ieee: M. Mondelli and A. Montanari, “Fundamental limits of weak recovery with applications to phase retrieval,” Foundations of Computational Mathematics, vol. 19, no. 3. Springer, pp. 703–773, 2019. ista: Mondelli M, Montanari A. 2019. Fundamental limits of weak recovery with applications to phase retrieval. Foundations of Computational Mathematics. 19(3), 703–773. mla: Mondelli, Marco, and Andrea Montanari. “Fundamental Limits of Weak Recovery with Applications to Phase Retrieval.” Foundations of Computational Mathematics, vol. 19, no. 3, Springer, 2019, pp. 703–73, doi:10.1007/s10208-018-9395-y. short: M. Mondelli, A. Montanari, Foundations of Computational Mathematics 19 (2019) 703–773. date_created: 2019-07-22T13:23:48Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:08:28Z day: '01' doi: 10.1007/s10208-018-9395-y extern: '1' external_id: arxiv: - '1708.05932' intvolume: ' 19' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.05932 month: '06' oa: 1 oa_version: Preprint page: 703-773 publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Fundamental limits of weak recovery with applications to phase retrieval type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '6672' abstract: - lang: eng text: The construction of anisotropic triangulations is desirable for various applications, such as the numerical solving of partial differential equations and the representation of surfaces in graphics. To solve this notoriously difficult problem in a practical way, we introduce the discrete Riemannian Voronoi diagram, a discrete structure that approximates the Riemannian Voronoi diagram. This structure has been implemented and was shown to lead to good triangulations in $\mathbb{R}^2$ and on surfaces embedded in $\mathbb{R}^3$ as detailed in our experimental companion paper. In this paper, we study theoretical aspects of our structure. Given a finite set of points $\mathcal{P}$ in a domain $\Omega$ equipped with a Riemannian metric, we compare the discrete Riemannian Voronoi diagram of $\mathcal{P}$ to its Riemannian Voronoi diagram. Both diagrams have dual structures called the discrete Riemannian Delaunay and the Riemannian Delaunay complex. We provide conditions that guarantee that these dual structures are identical. It then follows from previous results that the discrete Riemannian Delaunay complex can be embedded in $\Omega$ under sufficient conditions, leading to an anisotropic triangulation with curved simplices. Furthermore, we show that, under similar conditions, the simplices of this triangulation can be straightened. author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Mael full_name: Rouxel-Labbé, Mael last_name: Rouxel-Labbé - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Boissonnat J-D, Rouxel-Labbé M, Wintraecken M. Anisotropic triangulations via discrete Riemannian Voronoi diagrams. SIAM Journal on Computing. 2019;48(3):1046-1097. doi:10.1137/17m1152292 apa: Boissonnat, J.-D., Rouxel-Labbé, M., & Wintraecken, M. (2019). Anisotropic triangulations via discrete Riemannian Voronoi diagrams. SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM). https://doi.org/10.1137/17m1152292 chicago: Boissonnat, Jean-Daniel, Mael Rouxel-Labbé, and Mathijs Wintraecken. “Anisotropic Triangulations via Discrete Riemannian Voronoi Diagrams.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics (SIAM), 2019. https://doi.org/10.1137/17m1152292. ieee: J.-D. Boissonnat, M. Rouxel-Labbé, and M. Wintraecken, “Anisotropic triangulations via discrete Riemannian Voronoi diagrams,” SIAM Journal on Computing, vol. 48, no. 3. Society for Industrial & Applied Mathematics (SIAM), pp. 1046–1097, 2019. ista: Boissonnat J-D, Rouxel-Labbé M, Wintraecken M. 2019. Anisotropic triangulations via discrete Riemannian Voronoi diagrams. SIAM Journal on Computing. 48(3), 1046–1097. mla: Boissonnat, Jean-Daniel, et al. “Anisotropic Triangulations via Discrete Riemannian Voronoi Diagrams.” SIAM Journal on Computing, vol. 48, no. 3, Society for Industrial & Applied Mathematics (SIAM), 2019, pp. 1046–97, doi:10.1137/17m1152292. short: J.-D. Boissonnat, M. Rouxel-Labbé, M. Wintraecken, SIAM Journal on Computing 48 (2019) 1046–1097. date_created: 2019-07-24T08:42:12Z date_published: 2019-05-21T00:00:00Z date_updated: 2021-01-12T08:08:30Z day: '21' doi: 10.1137/17m1152292 extern: '1' external_id: arxiv: - '1703.06487' intvolume: ' 48' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.06487 month: '05' oa: 1 oa_version: Preprint page: 1046-1097 publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics (SIAM) quality_controlled: '1' status: public title: Anisotropic triangulations via discrete Riemannian Voronoi diagrams type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2019' ... --- _id: '6725' abstract: - lang: eng text: "A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds." alternative_title: - LIPIcs author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77' apa: 'Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77' chicago: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77. ieee: V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12. ista: 'Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP 2019: International Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.' mla: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77. short: V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12. conference: end_date: 2019-07-12 location: Patras, Greece name: 'ICALP 2019: International Colloquim on Automata, Languages and Programming' start_date: 2019-07-08 date_created: 2019-07-29T12:23:29Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:08:40Z day: '01' ddc: - '000' department: - _id: VlKo doi: 10.4230/LIPICS.ICALP.2019.77 ec_funded: 1 external_id: arxiv: - '1803.02289' file: - access_level: open_access checksum: f5ebee8eec6ae09e30365578ee63a492 content_type: application/pdf creator: dernst date_created: 2019-07-31T07:01:45Z date_updated: 2020-07-14T12:47:38Z file_id: '6738' file_name: 2019_LIPICS_Kolmogorov.pdf file_size: 575475 relation: main_file file_date_updated: 2020-07-14T12:47:38Z has_accepted_license: '1' intvolume: ' 132' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 77:1-77:12 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: 46th International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - 978-3-95977-109-2 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Testing the complexity of a valued CSP language tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 132 year: '2019' ... --- _id: '6726' abstract: - lang: eng text: Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so. article_processing_charge: No author: - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9' apa: 'Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9' chicago: 'Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.' ieee: 'M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.' ista: 'Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.' mla: Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9. short: M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180. conference: end_date: 2019-07-11 location: Rabat, Morocco name: 'AFRICACRYPT: International Conference on Cryptology in Africa' start_date: 2019-07-09 date_created: 2019-07-29T12:25:31Z date_published: 2019-06-29T00:00:00Z date_updated: 2023-02-23T12:50:15Z day: '29' department: - _id: KrPi doi: 10.1007/978-3-030-23696-0_9 ec_funded: 1 editor: - first_name: J full_name: Buchmann, J last_name: Buchmann - first_name: A full_name: Nitaj, A last_name: Nitaj - first_name: T full_name: Rachidi, T last_name: Rachidi intvolume: ' 11627' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/068 month: '06' oa: 1 oa_version: Preprint page: 157-180 place: Cham project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Progress in Cryptology – AFRICACRYPT 2019 publication_identifier: eisbn: - 978-3-0302-3696-0 isbn: - 978-3-0302-3695-3 issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Sampling the integers with low relative error type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11627 year: '2019' ... --- _id: '6663' abstract: - lang: eng text: Consider the problem of constructing a polar code of block length N for a given transmission channel W. Previous approaches require one to compute the reliability of the N synthetic channels and then use only those that are sufficiently reliable. However, we know from two independent works by Schürch and by Bardet et al. that the synthetic channels are partially ordered with respect to degradation. Hence, it is natural to ask whether the partial order can be exploited to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order, we can construct a polar code by computing the reliability of roughly a fraction 1/ log 3/2 N of the synthetic channels. In particular, we prove that N/ log 3/2 N is a lower bound on the number of synthetic channels to be considered and such a bound is tight up to a multiplicative factor log log N. This set of roughly N/ log 3/2 N synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists of reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general, and it can be used to further improve the complexity of the construction problem, in case a refined partial order on the synthetic channels of polar codes is discovered. author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Rudiger full_name: Urbanke, Rudiger last_name: Urbanke citation: ama: Mondelli M, Hassani H, Urbanke R. Construction of polar codes with sublinear complexity. IEEE. 2019;65(5):2782-2791. doi:10.1109/tit.2018.2889667 apa: Mondelli, M., Hassani, H., & Urbanke, R. (2019). Construction of polar codes with sublinear complexity. IEEE. IEEE. https://doi.org/10.1109/tit.2018.2889667 chicago: Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “Construction of Polar Codes with Sublinear Complexity.” IEEE. IEEE, 2019. https://doi.org/10.1109/tit.2018.2889667. ieee: M. Mondelli, H. Hassani, and R. Urbanke, “Construction of polar codes with sublinear complexity,” IEEE, vol. 65, no. 5. IEEE, pp. 2782–2791, 2019. ista: Mondelli M, Hassani H, Urbanke R. 2019. Construction of polar codes with sublinear complexity. IEEE. 65(5), 2782–2791. mla: Mondelli, Marco, et al. “Construction of Polar Codes with Sublinear Complexity.” IEEE, vol. 65, no. 5, IEEE, 2019, pp. 2782–91, doi:10.1109/tit.2018.2889667. short: M. Mondelli, H. Hassani, R. Urbanke, IEEE 65 (2019) 2782–2791. date_created: 2019-07-23T07:32:57Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-02-23T12:50:20Z day: '01' doi: 10.1109/tit.2018.2889667 extern: '1' external_id: arxiv: - '1612.05295' intvolume: ' 65' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.05295 month: '05' oa: 1 oa_version: Preprint page: 2782-2791 publication: IEEE publication_status: published publisher: IEEE quality_controlled: '1' related_material: record: - id: '6729' relation: earlier_version status: public status: public title: Construction of polar codes with sublinear complexity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2019' ... --- _id: '6747' abstract: - lang: eng text: "We establish connections between the problem of learning a two-layer neural network and tensor decomposition. We consider a model with feature vectors x∈ℝd, r hidden units with weights {wi}1≤i≤r and output y∈ℝ, i.e., y=∑ri=1σ(w\U0001D5B3ix), with activation functions given by low-degree polynomials. In particular, if σ(x)=a0+a1x+a3x3, we prove that no polynomial-time learning algorithm can outperform the trivial predictor that assigns to each example the response variable \U0001D53C(y), when d3/2≪r≪d2. Our conclusion holds for a `natural data distribution', namely standard Gaussian feature vectors x, and output distributed according to a two-layer neural network with random isotropic weights, and under a certain complexity-theoretic assumption on tensor decomposition. Roughly speaking, we assume that no polynomial-time algorithm can substantially outperform current methods for tensor decomposition based on the sum-of-squares hierarchy. We also prove generalizations of this statement for higher degree polynomial activations, and non-random weight vectors. Remarkably, several existing algorithms for learning two-layer networks with rigorous guarantees are based on tensor decomposition. Our results support the idea that this is indeed the core computational difficulty in learning such networks, under the stated generative model for the data. As a side result, we show that under this model learning the network requires accurate learning of its weights, a property that does not hold in a more general setting. " article_processing_charge: No author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Andrea full_name: Montanari, Andrea last_name: Montanari citation: ama: 'Mondelli M, Montanari A. On the connection between learning two-layers neural networks and tensor  decomposition. In: Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. Vol 89. Proceedings of Machine Learning Research; 2019:1051-1060.' apa: 'Mondelli, M., & Montanari, A. (2019). On the connection between learning two-layers neural networks and tensor  decomposition. In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (Vol. 89, pp. 1051–1060). Naha, Okinawa, Japan: Proceedings of Machine Learning Research.' chicago: Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor  Decomposition.” In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 89:1051–60. Proceedings of Machine Learning Research, 2019. ieee: M. Mondelli and A. Montanari, “On the connection between learning two-layers neural networks and tensor  decomposition,” in Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Naha, Okinawa, Japan, 2019, vol. 89, pp. 1051–1060. ista: 'Mondelli M, Montanari A. 2019. On the connection between learning two-layers neural networks and tensor  decomposition. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics vol. 89, 1051–1060.' mla: Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor  Decomposition.” Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, vol. 89, Proceedings of Machine Learning Research, 2019, pp. 1051–60. short: M. Mondelli, A. Montanari, in:, Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, 2019, pp. 1051–1060. conference: end_date: 2019-04-18 location: Naha, Okinawa, Japan name: 'AISTATS: Artificial Intelligence and Statistics' start_date: 2019-04-16 date_created: 2019-07-31T09:31:26Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T08:08:49Z day: '01' extern: '1' external_id: arxiv: - '1802.07301' intvolume: ' 89' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.07301 month: '04' oa: 1 oa_version: Preprint page: 1051-1060 publication: Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics publication_status: published publisher: Proceedings of Machine Learning Research quality_controlled: '1' status: public title: On the connection between learning two-layers neural networks and tensor decomposition type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2019' ... --- _id: '6750' abstract: - lang: eng text: 'Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. ' article_number: '8854897' article_processing_charge: No article_type: original author: - first_name: Seyyed Ali full_name: Hashemi, Seyyed Ali last_name: Hashemi - first_name: Carlo full_name: Condo, Carlo last_name: Condo - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Warren J full_name: Gross, Warren J last_name: Gross citation: ama: Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738 apa: Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738 chicago: Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738. ieee: S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019. ista: Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897. mla: Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738. short: S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019). date_created: 2019-07-31T09:51:14Z date_published: 2019-11-15T00:00:00Z date_updated: 2021-01-12T08:08:51Z day: '15' department: - _id: MaMo doi: 10.1109/TSP.2019.2944738 external_id: arxiv: - '1903.09203' intvolume: ' 67' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.09203 month: '11' oa: 1 oa_version: Preprint publication: IEEE Transactions on Signal Processing publication_identifier: issn: - 1053587X publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: Rate-flexible fast polar decoders type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 67 year: '2019' ... --- _id: '6759' abstract: - lang: eng text: "We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions." article_number: P3.17 article_processing_charge: No article_type: original author: - first_name: Vít full_name: Jelínek, Vít last_name: Jelínek - first_name: Martin full_name: Töpfer, Martin id: 4B865388-F248-11E8-B48F-1D18A9856A87 last_name: Töpfer citation: ama: Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096 apa: Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096 chicago: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096. ieee: V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019. ista: Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17. mla: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096. short: V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019). date_created: 2019-08-04T21:59:20Z date_published: 2019-07-19T00:00:00Z date_updated: 2022-03-18T12:32:02Z day: '19' ddc: - '510' department: - _id: DaAl doi: 10.37236/8096 ec_funded: 1 external_id: arxiv: - '1808.04148' file: - access_level: open_access checksum: 20fc366fc6683ef0b074a019b73a663a content_type: application/pdf creator: dernst date_created: 2019-08-05T06:46:55Z date_updated: 2020-07-14T12:47:39Z file_id: '6764' file_name: 2019_eJourCombinatorics_Jelinek.pdf file_size: 533697 relation: main_file file_date_updated: 2020-07-14T12:47:39Z has_accepted_license: '1' intvolume: ' 26' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Electronic Journal of Combinatorics publication_identifier: eissn: - '10778926' publication_status: published publisher: Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: On grounded L-graphs and their relatives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2019' ... --- _id: '6822' abstract: - lang: eng text: "In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher\r\nbidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called \r\n randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one." alternative_title: - LNCS author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Petr full_name: Novotny, Petr last_name: Novotny citation: ama: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision processes. In: Proceedings of the 13th International Conference of Reachability Problems. Vol 11674. Springer; 2019:1-12. doi:10.1007/978-3-030-30806-3_1' apa: 'Avni, G., Henzinger, T. A., Ibsen-Jensen, R., & Novotny, P. (2019). Bidding games on Markov decision processes. In Proceedings of the 13th International Conference of Reachability Problems (Vol. 11674, pp. 1–12). Brussels, Belgium: Springer. https://doi.org/10.1007/978-3-030-30806-3_1' chicago: Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding Games on Markov Decision Processes.” In Proceedings of the 13th International Conference of Reachability Problems, 11674:1–12. Springer, 2019. https://doi.org/10.1007/978-3-030-30806-3_1. ieee: G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games on Markov decision processes,” in Proceedings of the 13th International Conference of Reachability Problems, Brussels, Belgium, 2019, vol. 11674, pp. 1–12. ista: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov decision processes. Proceedings of the 13th International Conference of Reachability Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12.' mla: Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” Proceedings of the 13th International Conference of Reachability Problems, vol. 11674, Springer, 2019, pp. 1–12, doi:10.1007/978-3-030-30806-3_1. short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:, Proceedings of the 13th International Conference of Reachability Problems, Springer, 2019, pp. 1–12. conference: end_date: 2019-09-13 location: Brussels, Belgium name: 'RP: Reachability Problems' start_date: 2019-09-11 date_created: 2019-08-19T07:58:10Z date_published: 2019-09-06T00:00:00Z date_updated: 2021-01-12T08:09:12Z day: '06' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-30806-3_1 file: - access_level: open_access checksum: 45ebbc709af2b247d28c7c293c01504b content_type: application/pdf creator: gavni date_created: 2019-08-19T07:56:40Z date_updated: 2020-07-14T12:47:41Z file_id: '6823' file_name: prob.pdf file_size: 436635 relation: main_file file_date_updated: 2020-07-14T12:47:41Z has_accepted_license: '1' intvolume: ' 11674' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1-12 project: - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: ' Proceedings of the 13th International Conference of Reachability Problems' publication_identifier: isbn: - 978-303030805-6 issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: 1 status: public title: Bidding games on Markov decision processes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11674 year: '2019' ... --- _id: '6887' abstract: - lang: eng text: 'The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. ' alternative_title: - LIPIcs article_number: '7' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.7' apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In Leibniz International Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7' chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In Leibniz International Proceedings in Informatics, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7. ieee: K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in Leibniz International Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140. ista: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 7.' mla: Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” Leibniz International Proceedings in Informatics, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7. short: K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:07:58Z date_published: 2019-08-01T00:00:00Z date_updated: 2022-08-12T10:54:34Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.7 ec_funded: 1 file: - access_level: open_access checksum: e1f0e4061212454574f34a1368d018ec content_type: application/pdf creator: kschuh date_created: 2019-10-01T08:20:30Z date_updated: 2020-07-14T12:47:43Z file_id: '6922' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 730112 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Leibniz International Proceedings in Informatics publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Near-linear time algorithms for Streett objectives in graphs and MDPs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 140 year: '2019' ... --- _id: '6888' abstract: - lang: eng text: In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods. alternative_title: - ICRA article_number: '8793840' article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Manuel full_name: Zimmer, Manuel last_name: Zimmer - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: Proceedings - IEEE International Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840' apa: 'Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In Proceedings - IEEE International Conference on Robotics and Automation (Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840' chicago: Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In Proceedings - IEEE International Conference on Robotics and Automation, Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840. ieee: M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in Proceedings - IEEE International Conference on Robotics and Automation, Montreal, QC, Canada, 2019, vol. 2019–May. ista: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840.' mla: Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” Proceedings - IEEE International Conference on Robotics and Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840. short: M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019. conference: end_date: 2019-05-24 location: Montreal, QC, Canada name: 'ICRA: International Conference on Robotics and Automation' start_date: 2019-05-20 date_created: 2019-09-18T08:09:51Z date_published: 2019-05-01T00:00:00Z date_updated: 2021-01-12T08:09:28Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/icra.2019.8793840 file: - access_level: open_access checksum: f5545a6b60c3ffd01feb3613f81d03b6 content_type: application/pdf creator: dernst date_created: 2020-10-08T17:30:38Z date_updated: 2020-10-08T17:30:38Z file_id: '8636' file_name: 2019_ICRA_Lechner.pdf file_size: 3265107 relation: main_file success: 1 file_date_updated: 2020-10-08T17:30:38Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings - IEEE International Conference on Robotics and Automation publication_identifier: isbn: - '9781538660270' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Designing worm-inspired neural networks for interpretable robotic control type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 2019-May year: '2019' ... --- _id: '6886' abstract: - lang: eng text: 'In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. ' alternative_title: - LIPIcs article_number: '20' article_processing_charge: No author: - first_name: Milad full_name: Aghajohari, Milad last_name: Aghajohari - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20' apa: 'Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20' chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20. ieee: 'M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 20.' mla: Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.20. short: M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:06:58Z date_published: 2019-08-01T00:00:00Z date_updated: 2022-01-26T08:27:10Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.4230/LIPICS.CONCUR.2019.20 external_id: arxiv: - '1905.03588' file: - access_level: open_access checksum: 4df6d3575c506edb17215adada03cc8e content_type: application/pdf creator: kschuh date_created: 2019-09-27T12:21:38Z date_updated: 2020-07-14T12:47:43Z file_id: '6915' file_name: 2019_LIPIcs_Aghajohari.pdf file_size: 741425 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '08' oa: 1 oa_version: Published Version project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Determinacy in discrete-bidding infinite-duration games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 140 year: '2019' ... --- _id: '6885' abstract: - lang: eng text: 'A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. ' alternative_title: - LIPIcs article_number: '27' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.27' apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27. ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 27.' mla: Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:06:14Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:09:27Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.27 file: - access_level: open_access checksum: 4985e26e1572d1575d64d38acabd71d6 content_type: application/pdf creator: kschuh date_created: 2019-09-27T12:09:35Z date_updated: 2020-07-14T12:47:43Z file_id: '6914' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 538120 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Long-run average behavior of vector addition systems with states tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2019' ... --- _id: '6889' abstract: - lang: eng text: 'We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. ' alternative_title: - LIPIcs article_number: '6' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.6' apa: 'Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6' chicago: Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6. ieee: 'K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.' ista: 'Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6.' mla: Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6. short: K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-08-30 location: Amsterdam, Netherlands name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2019-08-27 date_created: 2019-09-18T08:11:43Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:09:28Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.4230/LIPICS.CONCUR.2019.6 file: - access_level: open_access checksum: 7b2ecfd4d9d02360308c0ca986fc10a7 content_type: application/pdf creator: kschuh date_created: 2019-10-01T08:49:45Z date_updated: 2020-07-14T12:47:43Z file_id: '6923' file_name: 2019_LIPIcs_Chatterjee.pdf file_size: 509163 relation: main_file file_date_updated: 2020-07-14T12:47:43Z has_accepted_license: '1' intvolume: ' 140' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Combinations of Qualitative Winning for Stochastic Parity Games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2019' ... --- _id: '6931' abstract: - lang: eng text: "Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures." alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Thomas full_name: Nowak, Thomas last_name: Nowak - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: ama: 'Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29' apa: 'Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs. In 33rd International Symposium on Distributed Computing (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.DISC.2019.29' chicago: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In 33rd International Symposium on Distributed Computing, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29. ieee: T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd International Symposium on Distributed Computing, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17. ista: 'Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.' mla: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” 33rd International Symposium on Distributed Computing, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29. short: T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17. conference: end_date: 2019-10-18 location: Budapest, Hungary name: 'DISC: International Symposium on Distributed Computing' start_date: 2019-10-14 date_created: 2019-10-08T12:41:38Z date_published: 2019-01-01T00:00:00Z date_updated: 2021-01-12T08:09:38Z ddc: - '004' department: - _id: DaAl doi: 10.4230/LIPICS.DISC.2019.29 ec_funded: 1 external_id: arxiv: - '1908.02743' file: - access_level: open_access checksum: 2d2202f90c6ac991e50876451627c4b5 content_type: application/pdf creator: jrybicki date_created: 2019-10-08T12:47:19Z date_updated: 2020-07-14T12:47:44Z file_id: '6934' file_name: LIPIcs-DISC-2019-29.pdf file_size: 639378 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 146' keyword: - consensus - approximate agreement - Byzantine faults - chordal graphs - lattice agreement language: - iso: eng oa: 1 oa_version: Published Version page: 29:1--29:17 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: 33rd International Symposium on Distributed Computing publication_identifier: eisbn: - 978-3-95977-126-9 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Byzantine approximate agreement on graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2019' ... --- _id: '6985' abstract: - lang: eng text: In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets. article_number: '8851954' author: - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Alexander full_name: Amini, Alexander last_name: Amini - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Felix full_name: Naser, Felix last_name: Naser - first_name: Radu full_name: Grosu, Radu last_name: Grosu - first_name: Daniela full_name: Rus, Daniela last_name: Rus citation: ama: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: Proceedings of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954' apa: 'Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In Proceedings of the International Joint Conference on Neural Networks. Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954' chicago: Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In Proceedings of the International Joint Conference on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954. ieee: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in Proceedings of the International Joint Conference on Neural Networks, Budapest, Hungary, 2019. ista: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.' mla: Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” Proceedings of the International Joint Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954. short: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019. conference: end_date: 2019-07-19 location: Budapest, Hungary name: 'IJCNN: International Joint Conference on Neural Networks' start_date: 2019-07-14 date_created: 2019-11-04T15:59:58Z date_published: 2019-09-30T00:00:00Z date_updated: 2021-01-12T08:11:19Z day: '30' department: - _id: ToHe doi: 10.1109/ijcnn.2019.8851954 external_id: arxiv: - '1809.03864' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.03864 month: '09' oa: 1 oa_version: Preprint publication: Proceedings of the International Joint Conference on Neural Networks publication_identifier: isbn: - '9781728119854' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: Response characterization for auditing cell dynamics in long short-term memory networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7007' abstract: - lang: eng text: 'We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.' article_number: '218' article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: S. Hamed full_name: Hassani, S. Hamed last_name: Hassani - first_name: Rüdiger full_name: Urbanke, Rüdiger last_name: Urbanke citation: ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218 apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218 chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218. ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019. ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218. mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218. short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019). date_created: 2019-11-12T14:46:19Z date_published: 2019-10-18T00:00:00Z date_updated: 2023-02-23T12:49:28Z day: '18' ddc: - '510' department: - _id: MaMo doi: 10.3390/a12100218 external_id: arxiv: - '1801.03153' file: - access_level: open_access checksum: 267756d8f9db572f496cd1663c89d59a content_type: application/pdf creator: dernst date_created: 2019-11-12T14:48:45Z date_updated: 2020-07-14T12:47:47Z file_id: '7008' file_name: 2019_Algorithms_Mondelli.pdf file_size: 696791 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 12' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Algorithms publication_identifier: issn: - 1999-4893 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '6675' relation: earlier_version status: public scopus_import: 1 status: public title: A new coding paradigm for the primitive relay channel tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '7035' abstract: - lang: eng text: 'The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.' article_processing_charge: No author: - first_name: Gyorgy Pal full_name: Geher, Gyorgy Pal last_name: Geher - first_name: Tamas full_name: Titkos, Tamas last_name: Titkos - first_name: Daniel full_name: Virosztek, Daniel id: 48DB45DA-F248-11E8-B48F-1D18A9856A87 last_name: Virosztek orcid: 0000-0003-1109-5511 citation: ama: 'Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.' apa: 'Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.' chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019. ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41. ista: Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41. mla: Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41. short: G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41. conference: end_date: 2019-01-30 location: Kyoto, Japan name: Research on isometries as preserver problems and related topics start_date: 2019-01-28 date_created: 2019-11-18T15:39:53Z date_published: 2019-01-30T00:00:00Z date_updated: 2021-01-12T08:11:33Z day: '30' department: - _id: LaEr intvolume: ' 2125' language: - iso: eng main_file_link: - open_access: '1' url: http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html month: '01' oa: 1 oa_version: Submitted Version page: 34-41 publication: Kyoto RIMS Kôkyûroku publication_status: published publisher: Research Institute for Mathematical Sciences, Kyoto University quality_controlled: '1' status: public title: Dirac masses and isometric rigidity type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2125 year: '2019' ... --- _id: '7055' abstract: - lang: eng text: A recent class of topological nodal-line semimetals with the general formula MSiX (M = Zr, Hf and X = S, Se, Te) has attracted much experimental and theoretical interest due to their properties, particularly their large magnetoresistances and high carrier mobilities. The plateletlike nature of the MSiX crystals and their extremely low residual resistivities make measurements of the resistivity along the [001] direction extremely challenging. To accomplish such measurements, microstructures of single crystals were prepared using focused ion beam techniques. Microstructures prepared in this manner have very well-defined geometries and maintain their high crystal quality, verified by the observations of quantum oscillations. We present magnetoresistance and quantum oscillation data for currents applied along both [001] and [100] in ZrSiS and ZrSiSe, which are consistent with the nontrivial topology of the Dirac line-node, as determined by a measured π Berry phase. Surprisingly, we find that, despite the three dimensional nature of both the Fermi surfaces of ZrSiS and ZrSiSe, both the resistivity anisotropy under applied magnetic fields and the in-plane angular dependent magnetoresistance differ considerably between the two compounds. Finally, we discuss the role microstructuring can play in the study of these materials and our ability to make these microstructures free-standing. article_number: '101116' article_processing_charge: No article_type: original author: - first_name: Kent R. full_name: Shirer, Kent R. last_name: Shirer - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Tino full_name: Zimmerling, Tino last_name: Zimmerling - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: Markus full_name: König, Markus last_name: König - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: Leslie full_name: Schoop, Leslie last_name: Schoop - first_name: Andrew P. full_name: Mackenzie, Andrew P. last_name: Mackenzie citation: ama: Shirer KR, Modic KA, Zimmerling T, et al. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 2019;7(10). doi:10.1063/1.5124568 apa: Shirer, K. R., Modic, K. A., Zimmerling, T., Bachmann, M. D., König, M., Moll, P. J. W., … Mackenzie, A. P. (2019). Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. AIP. https://doi.org/10.1063/1.5124568 chicago: Shirer, Kent R., Kimberly A Modic, Tino Zimmerling, Maja D. Bachmann, Markus König, Philip J. W. Moll, Leslie Schoop, and Andrew P. Mackenzie. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials. AIP, 2019. https://doi.org/10.1063/1.5124568. ieee: K. R. Shirer et al., “Out-of-plane transport in ZrSiS and ZrSiSe microstructures,” APL Materials, vol. 7, no. 10. AIP, 2019. ista: Shirer KR, Modic KA, Zimmerling T, Bachmann MD, König M, Moll PJW, Schoop L, Mackenzie AP. 2019. Out-of-plane transport in ZrSiS and ZrSiSe microstructures. APL Materials. 7(10), 101116. mla: Shirer, Kent R., et al. “Out-of-Plane Transport in ZrSiS and ZrSiSe Microstructures.” APL Materials, vol. 7, no. 10, 101116, AIP, 2019, doi:10.1063/1.5124568. short: K.R. Shirer, K.A. Modic, T. Zimmerling, M.D. Bachmann, M. König, P.J.W. Moll, L. Schoop, A.P. Mackenzie, APL Materials 7 (2019). date_created: 2019-11-19T12:52:43Z date_published: 2019-10-17T00:00:00Z date_updated: 2021-01-12T08:11:35Z day: '17' ddc: - '530' doi: 10.1063/1.5124568 extern: '1' file: - access_level: open_access checksum: 142fe7b3e37d8e916071743bb194360d content_type: application/pdf creator: dernst date_created: 2019-11-20T12:27:01Z date_updated: 2020-07-14T12:47:48Z file_id: '7087' file_name: 2019_APL_Shirer.pdf file_size: 2453220 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 7' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: APL Materials publication_identifier: issn: - 2166-532X publication_status: published publisher: AIP quality_controlled: '1' status: public title: Out-of-plane transport in ZrSiS and ZrSiSe microstructures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2019' ... --- _id: '7057' abstract: - lang: eng text: We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field. article_number: '2095' article_processing_charge: No article_type: original author: - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Tobias full_name: Meng, Tobias last_name: Meng - first_name: Filip full_name: Ronning, Filip last_name: Ronning - first_name: Eric D. full_name: Bauer, Eric D. last_name: Bauer - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw citation: ama: Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-38161-7 apa: Modic, K. A., Meng, T., Ronning, F., Bauer, E. D., Moll, P. J. W., & Ramshaw, B. J. (2019). Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-38161-7 chicago: Modic, Kimberly A, Tobias Meng, Filip Ronning, Eric D. Bauer, Philip J. W. Moll, and B. J. Ramshaw. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-018-38161-7. ieee: K. A. Modic, T. Meng, F. Ronning, E. D. Bauer, P. J. W. Moll, and B. J. Ramshaw, “Thermodynamic signatures of Weyl fermions in NbP,” Scientific Reports, vol. 9, no. 1. Springer Nature, 2019. ista: Modic KA, Meng T, Ronning F, Bauer ED, Moll PJW, Ramshaw BJ. 2019. Thermodynamic signatures of Weyl fermions in NbP. Scientific Reports. 9(1), 2095. mla: Modic, Kimberly A., et al. “Thermodynamic Signatures of Weyl Fermions in NbP.” Scientific Reports, vol. 9, no. 1, 2095, Springer Nature, 2019, doi:10.1038/s41598-018-38161-7. short: K.A. Modic, T. Meng, F. Ronning, E.D. Bauer, P.J.W. Moll, B.J. Ramshaw, Scientific Reports 9 (2019). date_created: 2019-11-19T13:00:35Z date_published: 2019-02-14T00:00:00Z date_updated: 2021-01-12T08:11:36Z day: '14' ddc: - '530' doi: 10.1038/s41598-018-38161-7 extern: '1' file: - access_level: open_access checksum: 3b5a7b316e1ff22aa0f89e8d1f1ace91 content_type: application/pdf creator: dernst date_created: 2019-11-20T12:24:13Z date_updated: 2020-07-14T12:47:48Z file_id: '7086' file_name: 2019_ScientificReports_Modic.pdf file_size: 3256400 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Thermodynamic signatures of Weyl fermions in NbP tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2019' ... --- _id: '7056' abstract: - lang: eng text: "In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have investigated a highly overdoped composition (x  =  0.56), prepared by a high-pressure, high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition at T N  =  120 K, well above the one at lower doping (0.15  <  x  <  0.27).\r\n\r\nBelow the onset of long-range magnetic order at T N, the electrical resistivity is strongly reduced and is dominated by electron–electron interactions, as evident from its temperature dependence. The Seebeck coefficient shows a clear metallic behavior as in narrow band conductors. The temperature dependence of the Hall coefficient and the violation of Kohler's rule agree with the multiband character of the material. No superconductivity was observed down to 1.8 K. The success of the high-pressure synthesis encourages further investigations of the so far only partially explored phase diagram in this family of Iron-based high temperature superconductors.\r\n" article_number: '485705' article_processing_charge: No article_type: original author: - first_name: Edoardo full_name: Martino, Edoardo last_name: Martino - first_name: Maja D full_name: Bachmann, Maja D last_name: Bachmann - first_name: Lidia full_name: Rossi, Lidia last_name: Rossi - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Ivica full_name: Zivkovic, Ivica last_name: Zivkovic - first_name: Henrik M full_name: Rønnow, Henrik M last_name: Rønnow - first_name: Philip J W full_name: Moll, Philip J W last_name: Moll - first_name: Ana full_name: Akrap, Ana last_name: Akrap - first_name: László full_name: Forró, László last_name: Forró - first_name: Sergiy full_name: Katrych, Sergiy last_name: Katrych citation: ama: 'Martino E, Bachmann MD, Rossi L, et al. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 2019;31(48). doi:10.1088/1361-648x/ab3b43' apa: 'Martino, E., Bachmann, M. D., Rossi, L., Modic, K. A., Zivkovic, I., Rønnow, H. M., … Katrych, S. (2019). Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648x/ab3b43' chicago: 'Martino, Edoardo, Maja D Bachmann, Lidia Rossi, Kimberly A Modic, Ivica Zivkovic, Henrik M Rønnow, Philip J W Moll, Ana Akrap, László Forró, and Sergiy Katrych. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter. IOP Publishing, 2019. https://doi.org/10.1088/1361-648x/ab3b43.' ieee: 'E. Martino et al., “Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2,” Journal of Physics: Condensed Matter, vol. 31, no. 48. IOP Publishing, 2019.' ista: 'Martino E, Bachmann MD, Rossi L, Modic KA, Zivkovic I, Rønnow HM, Moll PJW, Akrap A, Forró L, Katrych S. 2019. Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2. Journal of Physics: Condensed Matter. 31(48), 485705.' mla: 'Martino, Edoardo, et al. “Persistent Antiferromagnetic Order in Heavily Overdoped Ca1−x La x FeAs2.” Journal of Physics: Condensed Matter, vol. 31, no. 48, 485705, IOP Publishing, 2019, doi:10.1088/1361-648x/ab3b43.' short: 'E. Martino, M.D. Bachmann, L. Rossi, K.A. Modic, I. Zivkovic, H.M. Rønnow, P.J.W. Moll, A. Akrap, L. Forró, S. Katrych, Journal of Physics: Condensed Matter 31 (2019).' date_created: 2019-11-19T12:56:17Z date_published: 2019-09-03T00:00:00Z date_updated: 2021-01-12T08:11:35Z day: '03' doi: 10.1088/1361-648x/ab3b43 extern: '1' external_id: arxiv: - '1905.08640' intvolume: ' 31' issue: '48' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.08640 month: '09' oa: 1 oa_version: Preprint publication: 'Journal of Physics: Condensed Matter' publication_identifier: eissn: - 1361-648X issn: - 0953-8984 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2019' ... --- _id: '7082' abstract: - lang: eng text: Although crystals of strongly correlated metals exhibit a diverse set of electronic ground states, few approaches exist for spatially modulating their properties. In this study, we demonstrate disorder-free control, on the micrometer scale, over the superconducting state in samples of the heavy-fermion superconductor CeIrIn5. We pattern crystals by focused ion beam milling to tailor the boundary conditions for the elastic deformation upon thermal contraction during cooling. The resulting nonuniform strain fields induce complex patterns of superconductivity, owing to the strong dependence of the transition temperature on the strength and direction of strain. These results showcase a generic approach to manipulating electronic order on micrometer length scales in strongly correlated matter without compromising the cleanliness, stoichiometry, or mean free path. article_processing_charge: No article_type: original author: - first_name: Maja D. full_name: Bachmann, Maja D. last_name: Bachmann - first_name: G. M. full_name: Ferguson, G. M. last_name: Ferguson - first_name: Florian full_name: Theuss, Florian last_name: Theuss - first_name: Tobias full_name: Meng, Tobias last_name: Meng - first_name: Carsten full_name: Putzke, Carsten last_name: Putzke - first_name: Toni full_name: Helm, Toni last_name: Helm - first_name: K. R. full_name: Shirer, K. R. last_name: Shirer - first_name: You-Sheng full_name: Li, You-Sheng last_name: Li - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Michael full_name: Nicklas, Michael last_name: Nicklas - first_name: Markus full_name: König, Markus last_name: König - first_name: D. full_name: Low, D. last_name: Low - first_name: Sayak full_name: Ghosh, Sayak last_name: Ghosh - first_name: Andrew P. full_name: Mackenzie, Andrew P. last_name: Mackenzie - first_name: Frank full_name: Arnold, Frank last_name: Arnold - first_name: Elena full_name: Hassinger, Elena last_name: Hassinger - first_name: Ross D. full_name: McDonald, Ross D. last_name: McDonald - first_name: Laurel E. full_name: Winter, Laurel E. last_name: Winter - first_name: Eric D. full_name: Bauer, Eric D. last_name: Bauer - first_name: Filip full_name: Ronning, Filip last_name: Ronning - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw - first_name: Katja C. full_name: Nowack, Katja C. last_name: Nowack - first_name: Philip J. W. full_name: Moll, Philip J. W. last_name: Moll citation: ama: Bachmann MD, Ferguson GM, Theuss F, et al. Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. 2019;366(6462):221-226. doi:10.1126/science.aao6640 apa: Bachmann, M. D., Ferguson, G. M., Theuss, F., Meng, T., Putzke, C., Helm, T., … Moll, P. J. W. (2019). Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. AAAS. https://doi.org/10.1126/science.aao6640 chicago: Bachmann, Maja D., G. M. Ferguson, Florian Theuss, Tobias Meng, Carsten Putzke, Toni Helm, K. R. Shirer, et al. “Spatial Control of Heavy-Fermion Superconductivity in CeIrIn5.” Science. AAAS, 2019. https://doi.org/10.1126/science.aao6640. ieee: M. D. Bachmann et al., “Spatial control of heavy-fermion superconductivity in CeIrIn5,” Science, vol. 366, no. 6462. AAAS, pp. 221–226, 2019. ista: Bachmann MD, Ferguson GM, Theuss F, Meng T, Putzke C, Helm T, Shirer KR, Li Y-S, Modic KA, Nicklas M, König M, Low D, Ghosh S, Mackenzie AP, Arnold F, Hassinger E, McDonald RD, Winter LE, Bauer ED, Ronning F, Ramshaw BJ, Nowack KC, Moll PJW. 2019. Spatial control of heavy-fermion superconductivity in CeIrIn5. Science. 366(6462), 221–226. mla: Bachmann, Maja D., et al. “Spatial Control of Heavy-Fermion Superconductivity in CeIrIn5.” Science, vol. 366, no. 6462, AAAS, 2019, pp. 221–26, doi:10.1126/science.aao6640. short: M.D. Bachmann, G.M. Ferguson, F. Theuss, T. Meng, C. Putzke, T. Helm, K.R. Shirer, Y.-S. Li, K.A. Modic, M. Nicklas, M. König, D. Low, S. Ghosh, A.P. Mackenzie, F. Arnold, E. Hassinger, R.D. McDonald, L.E. Winter, E.D. Bauer, F. Ronning, B.J. Ramshaw, K.C. Nowack, P.J.W. Moll, Science 366 (2019) 221–226. date_created: 2019-11-19T13:55:58Z date_published: 2019-10-11T00:00:00Z date_updated: 2021-01-12T08:11:46Z day: '11' doi: 10.1126/science.aao6640 extern: '1' intvolume: ' 366' issue: '6462' language: - iso: eng month: '10' oa_version: None page: 221-226 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' status: public title: Spatial control of heavy-fermion superconductivity in CeIrIn5 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 366 year: '2019' ... --- _id: '7128' abstract: - lang: eng text: Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation. article_processing_charge: Yes article_type: original author: - first_name: Consuelo full_name: Torrini, Consuelo last_name: Torrini - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Ellen full_name: Dirkx, Ellen last_name: Dirkx - first_name: Luca full_name: Braga, Luca last_name: Braga - first_name: Hashim full_name: Ali, Hashim last_name: Ali - first_name: Giulia full_name: Prosdocimo, Giulia last_name: Prosdocimo - first_name: Maria Ines full_name: Gutierrez, Maria Ines last_name: Gutierrez - first_name: Chiara full_name: Collesi, Chiara last_name: Collesi - first_name: Danilo full_name: Licastro, Danilo last_name: Licastro - first_name: Lorena full_name: Zentilin, Lorena last_name: Zentilin - first_name: Miguel full_name: Mano, Miguel last_name: Mano - first_name: Serena full_name: Zacchigna, Serena last_name: Zacchigna - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Areejit full_name: Samal, Areejit last_name: Samal - first_name: Mauro full_name: Giacca, Mauro last_name: Giacca citation: ama: Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 2019;27(9):2759-2771.e5. doi:10.1016/j.celrep.2019.05.005 apa: Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G., … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2019.05.005 chicago: Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali, Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports. Elsevier, 2019. https://doi.org/10.1016/j.celrep.2019.05.005. ieee: C. Torrini et al., “Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation,” Cell Reports, vol. 27, no. 9. Elsevier, p. 2759–2771.e5, 2019. ista: Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5. mla: Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” Cell Reports, vol. 27, no. 9, Elsevier, 2019, p. 2759–2771.e5, doi:10.1016/j.celrep.2019.05.005. short: C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5. date_created: 2019-11-26T22:30:07Z date_published: 2019-05-28T00:00:00Z date_updated: 2021-01-12T08:11:56Z day: '28' ddc: - '576' doi: 10.1016/j.celrep.2019.05.005 extern: '1' external_id: pmid: - '31141697' file: - access_level: open_access checksum: c5d855d07263bfec718673385d0ea2d7 content_type: application/pdf creator: rcubero date_created: 2019-11-26T22:30:43Z date_updated: 2020-07-14T12:47:50Z file_id: '7129' file_name: torrini_cellreports_2019.pdf file_size: 4650750 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 27' issue: '9' keyword: - cardiomyocyte - cell cycle - Cofilin2 - cytoskeleton - Hippo - microRNA - regeneration - YAP language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 2759-2771.e5 pmid: 1 publication: Cell Reports publication_identifier: issn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2019' ... --- _id: '7130' abstract: - lang: eng text: "We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples." acknowledgement: We acknowledge interesting discussions with M Abbott, E Aurell, J Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part, by the ICTP through the OEA-AC-98 (JS). article_number: '063402' article_processing_charge: No article_type: original author: - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Junghyo full_name: Jo, Junghyo last_name: Jo - first_name: Matteo full_name: Marsili, Matteo last_name: Marsili - first_name: Yasser full_name: Roudi, Yasser last_name: Roudi - first_name: Juyong full_name: Song, Juyong last_name: Song citation: ama: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019;2019(6). doi:10.1088/1742-5468/ab16c8' apa: 'Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., & Song, J. (2019). Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab16c8' chicago: 'Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song. “Statistical Criticality Arises in Most Informative Representations.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2019. https://doi.org/10.1088/1742-5468/ab16c8.' ieee: 'R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality arises in most informative representations,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6. IOP Publishing, 2019.' ista: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063402.' mla: 'Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative Representations.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:10.1088/1742-5468/ab16c8.' short: 'R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).' date_created: 2019-11-26T22:36:09Z date_published: 2019-06-17T00:00:00Z date_updated: 2021-01-12T08:11:57Z day: '17' doi: 10.1088/1742-5468/ab16c8 extern: '1' external_id: arxiv: - '1808.00249' intvolume: ' 2019' issue: '6' keyword: - optimization under uncertainty - source coding - large deviation language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.00249 month: '06' oa: 1 oa_version: Preprint publication: 'Journal of Statistical Mechanics: Theory and Experiment' publication_identifier: issn: - 1742-5468 publication_status: published publisher: IOP Publishing quality_controlled: '1' status: public title: Statistical criticality arises in most informative representations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2019 year: '2019' ... --- _id: '7150' abstract: - lang: eng text: "In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:\r\n\r\n1. triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.\r\n \r\nIn addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles." article_processing_charge: No article_type: original author: - first_name: Keren full_name: Censor-Hillel, Keren last_name: Censor-Hillel - first_name: Petteri full_name: Kaski, Petteri last_name: Kaski - first_name: Janne full_name: Korhonen, Janne id: C5402D42-15BC-11E9-A202-CA2BE6697425 last_name: Korhonen - first_name: Christoph full_name: Lenzen, Christoph last_name: Lenzen - first_name: Ami full_name: Paz, Ami last_name: Paz - first_name: Jukka full_name: Suomela, Jukka last_name: Suomela citation: ama: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic methods in the congested clique. Distributed Computing. 2019;32(6):461-478. doi:10.1007/s00446-016-0270-2 apa: Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., & Suomela, J. (2019). Algebraic methods in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-016-0270-2 chicago: Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen, Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” Distributed Computing. Springer Nature, 2019. https://doi.org/10.1007/s00446-016-0270-2. ieee: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela, “Algebraic methods in the congested clique,” Distributed Computing, vol. 32, no. 6. Springer Nature, pp. 461–478, 2019. ista: Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic methods in the congested clique. Distributed Computing. 32(6), 461–478. mla: Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” Distributed Computing, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:10.1007/s00446-016-0270-2. short: K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed Computing 32 (2019) 461–478. date_created: 2019-12-05T09:49:49Z date_published: 2019-12-01T00:00:00Z date_updated: 2021-01-12T08:12:05Z day: '01' doi: 10.1007/s00446-016-0270-2 extern: '1' external_id: arxiv: - '1503.04963' intvolume: ' 32' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1503.04963 month: '12' oa: 1 oa_version: Preprint page: 461-478 publication: Distributed Computing publication_identifier: issn: - 0178-2770 - 1432-0452 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Algebraic methods in the congested clique type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2019' ... --- _id: '7171' abstract: - lang: ger text: "Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!" article_processing_charge: No citation: ama: 'Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019. doi:10.1007/978-3-658-26763-6' apa: 'Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden: Springer Nature. https://doi.org/10.1007/978-3-658-26763-6' chicago: 'Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.' ieee: 'K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature, 2019.' ista: 'Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.' mla: 'Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.' short: 'K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.' date_created: 2019-12-11T14:15:56Z date_published: 2019-10-30T00:00:00Z date_updated: 2021-12-22T14:40:58Z day: '30' department: - _id: ChLa doi: 10.1007/978-3-658-26763-6 edition: '1' editor: - first_name: Kristian full_name: Kersting, Kristian last_name: Kersting - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Constantin full_name: Rothkopf, Constantin last_name: Rothkopf language: - iso: ger month: '10' oa_version: None page: XIV, 245 place: Wiesbaden publication_identifier: eisbn: - 978-3-658-26763-6 isbn: - 978-3-658-26762-9 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Website relation: press_release url: https://ist.ac.at/en/news/book-release-how-machines-learn/ status: public title: 'Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt' type: book_editor user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '7275' abstract: - lang: eng text: Aprotic alkali metal–oxygen batteries require reversible formation of metal superoxide or peroxide on cycling. Severe parasitic reactions cause poor rechargeability, efficiency, and cycle life and have been shown to be caused by singlet oxygen (1O2) that forms at all stages of cycling. However, its formation mechanism remains unclear. We show that disproportionation of superoxide, the product or intermediate on discharge and charge, to peroxide and oxygen is responsible for 1O2 formation. While the overall reaction is driven by the stability of peroxide and thus favored by stronger Lewis acidic cations such as Li+, the 1O2 fraction is enhanced by weak Lewis acids such as organic cations. Concurrently, the metal peroxide yield drops with increasing 1O2. The results explain a major parasitic pathway during cell cycling and the growing severity in K–, Na–, and Li–O2 cells based on the growing propensity for disproportionation. High capacities and rates with peroxides are now realized to require solution processes, which form peroxide or release O2via disproportionation. The results therefore establish the central dilemma that disproportionation is required for high capacity but also responsible for irreversible reactions. Highly reversible cell operation requires hence finding reaction routes that avoid disproportionation. article_processing_charge: No article_type: original author: - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Riccardo full_name: Spezia, Riccardo last_name: Spezia - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: Francesco F. full_name: Summa, Francesco F. last_name: Summa - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Olivier full_name: Fontaine, Olivier last_name: Fontaine - first_name: Sergio full_name: Brutti, Sergio last_name: Brutti - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mourad E, Petit YK, Spezia R, et al. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. 2019;12(8):2559-2568. doi:10.1039/c9ee01453e apa: Mourad, E., Petit, Y. K., Spezia, R., Samojlov, A., Summa, F. F., Prehal, C., … Freunberger, S. A. (2019). Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. RSC. https://doi.org/10.1039/c9ee01453e chicago: Mourad, Eléonore, Yann K. Petit, Riccardo Spezia, Aleksej Samojlov, Francesco F. Summa, Christian Prehal, Christian Leypold, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” Energy & Environmental Science. RSC, 2019. https://doi.org/10.1039/c9ee01453e. ieee: E. Mourad et al., “Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries,” Energy & Environmental Science, vol. 12, no. 8. RSC, pp. 2559–2568, 2019. ista: Mourad E, Petit YK, Spezia R, Samojlov A, Summa FF, Prehal C, Leypold C, Mahne N, Slugovc C, Fontaine O, Brutti S, Freunberger SA. 2019. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. 12(8), 2559–2568. mla: Mourad, Eléonore, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” Energy & Environmental Science, vol. 12, no. 8, RSC, 2019, pp. 2559–68, doi:10.1039/c9ee01453e. short: E. Mourad, Y.K. Petit, R. Spezia, A. Samojlov, F.F. Summa, C. Prehal, C. Leypold, N. Mahne, C. Slugovc, O. Fontaine, S. Brutti, S.A. Freunberger, Energy & Environmental Science 12 (2019) 2559–2568. date_created: 2020-01-15T07:18:04Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:12:41Z day: '01' ddc: - '530' - '541' - '540' doi: 10.1039/c9ee01453e extern: '1' file: - access_level: open_access checksum: 94d4cfb2ab0b4c90ef76a7f3cc811feb content_type: application/pdf creator: dernst date_created: 2020-01-30T16:11:05Z date_updated: 2020-07-14T12:47:55Z file_id: '7424' file_name: 2019_EnergyEnvironScienc_Mourad.pdf file_size: 2888027 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 12' issue: '8' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '08' oa: 1 oa_version: Published Version page: 2559-2568 publication: Energy & Environmental Science publication_identifier: issn: - 1754-5692 - 1754-5706 publication_status: published publisher: RSC quality_controlled: '1' status: public title: Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '7280' abstract: - lang: eng text: Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during discharge and oxidizing it during recharge. The significant problem of oxidizing the solid insulating lithium peroxide can greatly be facilitated by incorporating redox mediators that shuttle electron-holes between the porous substrate and lithium peroxide. Redox mediator stability is thus key for energy efficiency, reversibility, and cycle life. However, the gradual deactivation of redox mediators during repeated cycling has not conclusively been explained. Here, we show that organic redox mediators are predominantly decomposed by singlet oxygen that forms during cycling. Their reaction with superoxide, previously assumed to mainly trigger their degradation, peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced form of the mediator is markedly more reactive towards singlet oxygen than the oxidized form, from which we derive reaction mechanisms supported by density functional theory calculations. Redox mediators must thus be designed for stability against singlet oxygen. article_number: '1380' article_processing_charge: No article_type: original author: - first_name: Won-Jin full_name: Kwak, Won-Jin last_name: Kwak - first_name: Hun full_name: Kim, Hun last_name: Kim - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Trung Thien full_name: Nguyen, Trung Thien last_name: Nguyen - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Paul full_name: Redfern, Paul last_name: Redfern - first_name: Larry A. full_name: Curtiss, Larry A. last_name: Curtiss - first_name: Hun-Gi full_name: Jung, Hun-Gi last_name: Jung - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun citation: ama: Kwak W-J, Kim H, Petit YK, et al. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 2019;10. doi:10.1038/s41467-019-09399-0 apa: Kwak, W.-J., Kim, H., Petit, Y. K., Leypold, C., Nguyen, T. T., Mahne, N., … Sun, Y.-K. (2019). Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09399-0 chicago: Kwak, Won-Jin, Hun Kim, Yann K. Petit, Christian Leypold, Trung Thien Nguyen, Nika Mahne, Paul Redfern, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09399-0. ieee: W.-J. Kwak et al., “Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Kwak W-J, Kim H, Petit YK, Leypold C, Nguyen TT, Mahne N, Redfern P, Curtiss LA, Jung H-G, Borisov SM, Freunberger SA, Sun Y-K. 2019. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 10, 1380. mla: Kwak, Won-Jin, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications, vol. 10, 1380, Springer Nature, 2019, doi:10.1038/s41467-019-09399-0. short: W.-J. Kwak, H. Kim, Y.K. Petit, C. Leypold, T.T. Nguyen, N. Mahne, P. Redfern, L.A. Curtiss, H.-G. Jung, S.M. Borisov, S.A. Freunberger, Y.-K. Sun, Nature Communications 10 (2019). date_created: 2020-01-15T12:12:26Z date_published: 2019-03-26T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '26' ddc: - '540' doi: 10.1038/s41467-019-09399-0 extern: '1' file: - access_level: open_access checksum: 123dd33e7f26761c82c74e10811a1e4d content_type: application/pdf creator: dernst date_created: 2020-01-22T15:58:54Z date_updated: 2020-07-14T12:47:55Z file_id: '7355' file_name: 2019_NatureComm_Kwak.pdf file_size: 1003676 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 10' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '7276' abstract: - lang: eng text: Singlet oxygen (1O2) causes a major fraction of the parasitic chemistry during the cycling of non‐aqueous alkali metal‐O2 batteries and also contributes to interfacial reactivity of transition‐metal oxide intercalation compounds. We introduce DABCOnium, the mono alkylated form of 1,4‐diazabicyclo[2.2.2]octane (DABCO), as an efficient 1O2 quencher with an unusually high oxidative stability of ca. 4.2 V vs. Li/Li+. Previous quenchers are strongly Lewis basic amines with too low oxidative stability. DABCOnium is an ionic liquid, non‐volatile, highly soluble in the electrolyte, stable against superoxide and peroxide, and compatible with lithium metal. The electrochemical stability covers the required range for metal–O2 batteries and greatly reduces 1O2 related parasitic chemistry as demonstrated for the Li–O2 cell. article_processing_charge: No article_type: original author: - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: 'Petit YK, Leypold C, Mahne N, et al. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 2019;58(20):6535-6539. doi:10.1002/anie.201901869' apa: 'Petit, Y. K., Leypold, C., Mahne, N., Mourad, E., Schafzahl, L., Slugovc, C., … Freunberger, S. A. (2019). DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201901869' chicago: 'Petit, Yann K., Christian Leypold, Nika Mahne, Eléonore Mourad, Lukas Schafzahl, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition. Wiley, 2019. https://doi.org/10.1002/anie.201901869.' ieee: 'Y. K. Petit et al., “DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells,” Angewandte Chemie International Edition, vol. 58, no. 20. Wiley, pp. 6535–6539, 2019.' ista: 'Petit YK, Leypold C, Mahne N, Mourad E, Schafzahl L, Slugovc C, Borisov SM, Freunberger SA. 2019. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 58(20), 6535–6539.' mla: 'Petit, Yann K., et al. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition, vol. 58, no. 20, Wiley, 2019, pp. 6535–39, doi:10.1002/anie.201901869.' short: Y.K. Petit, C. Leypold, N. Mahne, E. Mourad, L. Schafzahl, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie International Edition 58 (2019) 6535–6539. date_created: 2020-01-15T07:19:27Z date_published: 2019-05-13T00:00:00Z date_updated: 2021-01-12T08:12:42Z day: '13' ddc: - '540' doi: 10.1002/anie.201901869 extern: '1' file: - access_level: open_access checksum: 9620b6a511a910d7abe1f26c42dc7f83 content_type: application/pdf creator: dernst date_created: 2020-01-22T16:16:54Z date_updated: 2020-07-14T12:47:55Z file_id: '7356' file_name: 2019_AngewChemie_Petit.pdf file_size: 952737 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 58' issue: '20' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 6535-6539 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2019' ... --- _id: '7281' abstract: - lang: eng text: Li–O2 batteries are plagued by side reactions that cause poor rechargeability and efficiency. These reactions were recently revealed to be predominantly caused by singlet oxygen, which can be neutralized by chemical traps or physical quenchers. However, traps are irreversibly consumed and thus only active for a limited time, and so far identified quenchers lack oxidative stability to be suitable for typically required recharge potentials. Thus, reducing the charge potential within the stability limit of the quencher and/or finding more stable quenchers is required. Here, we show that dimethylphenazine as a redox mediator decreases the charge potential well within the stability limit of the quencher 1,4-diazabicyclo[2.2.2]octane. The quencher can thus mitigate the parasitic reactions without being oxidatively decomposed. At the same time the quencher protects the redox mediator from singlet oxygen attack. The mutual conservation of the redox mediator and the quencher is rational for stable and effective Li–O2 batteries. article_processing_charge: No article_type: original author: - first_name: Won-Jin full_name: Kwak, Won-Jin last_name: Kwak - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Hun full_name: Kim, Hun last_name: Kim - first_name: Jiwon full_name: Park, Jiwon last_name: Park - first_name: Trung Thien full_name: Nguyen, Trung Thien last_name: Nguyen - first_name: Hun-Gi full_name: Jung, Hun-Gi last_name: Jung - first_name: Hye Ryung full_name: Byon, Hye Ryung last_name: Byon - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun citation: ama: Kwak W-J, Freunberger SA, Kim H, et al. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 2019;9(11):9914-9922. doi:10.1021/acscatal.9b01337 apa: Kwak, W.-J., Freunberger, S. A., Kim, H., Park, J., Nguyen, T. T., Jung, H.-G., … Sun, Y.-K. (2019). Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. ACS. https://doi.org/10.1021/acscatal.9b01337 chicago: Kwak, Won-Jin, Stefan Alexander Freunberger, Hun Kim, Jiwon Park, Trung Thien Nguyen, Hun-Gi Jung, Hye Ryung Byon, and Yang-Kook Sun. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis. ACS, 2019. https://doi.org/10.1021/acscatal.9b01337. ieee: W.-J. Kwak et al., “Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries,” ACS Catalysis, vol. 9, no. 11. ACS, pp. 9914–9922, 2019. ista: Kwak W-J, Freunberger SA, Kim H, Park J, Nguyen TT, Jung H-G, Byon HR, Sun Y-K. 2019. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 9(11), 9914–9922. mla: Kwak, Won-Jin, et al. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis, vol. 9, no. 11, ACS, 2019, pp. 9914–22, doi:10.1021/acscatal.9b01337. short: W.-J. Kwak, S.A. Freunberger, H. Kim, J. Park, T.T. Nguyen, H.-G. Jung, H.R. Byon, Y.-K. Sun, ACS Catalysis 9 (2019) 9914–9922. date_created: 2020-01-15T12:12:40Z date_published: 2019-11-01T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '01' ddc: - '540' doi: 10.1021/acscatal.9b01337 extern: '1' file: - access_level: open_access checksum: bbaebfe5ff0bcab6235821ba3460b7de content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T15:19:30Z date_updated: 2020-07-14T12:47:55Z file_id: '8053' file_name: Revised Manuscript.pdf file_size: 1199086 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 9914-9922 publication: ACS Catalysis publication_identifier: issn: - 2155-5435 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2019' ... --- _id: '7282' abstract: - lang: eng text: Interphases that form on the anode surface of lithium-ion batteries are critical for performance and lifetime, but are poorly understood. Now, a decade-old misconception regarding a main component of the interphase has been revealed, which could potentially lead to improved devices. article_processing_charge: No article_type: letter_note author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Freunberger SA. Interphase identity crisis. Nature Chemistry. 2019;11(9):761-763. doi:10.1038/s41557-019-0311-0 apa: Freunberger, S. A. (2019). Interphase identity crisis. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-019-0311-0 chicago: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry. Springer Nature, 2019. https://doi.org/10.1038/s41557-019-0311-0. ieee: S. A. Freunberger, “Interphase identity crisis,” Nature Chemistry, vol. 11, no. 9. Springer Nature, pp. 761–763, 2019. ista: Freunberger SA. 2019. Interphase identity crisis. Nature Chemistry. 11(9), 761–763. mla: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry, vol. 11, no. 9, Springer Nature, 2019, pp. 761–63, doi:10.1038/s41557-019-0311-0. short: S.A. Freunberger, Nature Chemistry 11 (2019) 761–763. date_created: 2020-01-15T12:12:53Z date_published: 2019-08-19T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '19' ddc: - '540' - '547' doi: 10.1038/s41557-019-0311-0 extern: '1' file: - access_level: open_access checksum: 76806cff3d5b62f846499a8617cee7ef content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T15:38:21Z date_updated: 2020-07-14T12:47:55Z file_id: '8054' file_name: Freunberger on Eichhorn.pdf file_size: 286805 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 11' issue: '9' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 761-763 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Interphase identity crisis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2019' ... --- _id: '7283' abstract: - lang: eng text: Potassium–air batteries, which suffer from oxygen cathode and potassium metal anode degradation, can be cycled thousands of times when an organic anode replaces the metal. article_processing_charge: No article_type: letter_note author: - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Petit YK, Freunberger SA. Thousands of cycles. Nature Materials. 2019;18(4):301-302. doi:10.1038/s41563-019-0313-8 apa: Petit, Y. K., & Freunberger, S. A. (2019). Thousands of cycles. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-019-0313-8 chicago: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials. Springer Nature, 2019. https://doi.org/10.1038/s41563-019-0313-8. ieee: Y. K. Petit and S. A. Freunberger, “Thousands of cycles,” Nature Materials, vol. 18, no. 4. Springer Nature, pp. 301–302, 2019. ista: Petit YK, Freunberger SA. 2019. Thousands of cycles. Nature Materials. 18(4), 301–302. mla: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials, vol. 18, no. 4, Springer Nature, 2019, pp. 301–02, doi:10.1038/s41563-019-0313-8. short: Y.K. Petit, S.A. Freunberger, Nature Materials 18 (2019) 301–302. date_created: 2020-01-15T12:13:05Z date_published: 2019-03-20T00:00:00Z date_updated: 2021-01-12T08:12:45Z day: '20' ddc: - '540' - '541' doi: 10.1038/s41563-019-0313-8 extern: '1' file: - access_level: open_access checksum: 4c9a0314327028a22dd902bc109b8798 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T16:26:54Z date_updated: 2020-07-14T12:47:55Z file_id: '8059' file_name: NaV_final.pdf file_size: 398123 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 18' issue: '4' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 301-302 publication: Nature Materials publication_identifier: issn: - 1476-1122 - 1476-4660 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Thousands of cycles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2019' ... --- _id: '7284' abstract: - lang: eng text: In this issue of Joule, Dongmin Im and coworkers from Samsung in South Korea describe a prototype lithium-O2 battery that reaches ∼700 Wh kg–1 and ∼600 Wh L–1 on the cell level. They cut all components to the minimum to reach this value. Difficulties filling the pores with discharge product and inhomogeneous cell utilization turn out to limit the achievable energy. Their work underlines the importance of reporting performance with respect to full cell weight and volume. article_processing_charge: No article_type: review author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Freunberger SA. Li-O2 cell-scale energy densities. Joule. 2019;3(2):321-323. doi:10.1016/j.joule.2019.01.020 apa: Prehal, C., & Freunberger, S. A. (2019). Li-O2 cell-scale energy densities. Joule. Elsevier. https://doi.org/10.1016/j.joule.2019.01.020 chicago: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule. Elsevier, 2019. https://doi.org/10.1016/j.joule.2019.01.020. ieee: C. Prehal and S. A. Freunberger, “Li-O2 cell-scale energy densities,” Joule, vol. 3, no. 2. Elsevier, pp. 321–323, 2019. ista: Prehal C, Freunberger SA. 2019. Li-O2 cell-scale energy densities. Joule. 3(2), 321–323. mla: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule, vol. 3, no. 2, Elsevier, 2019, pp. 321–23, doi:10.1016/j.joule.2019.01.020. short: C. Prehal, S.A. Freunberger, Joule 3 (2019) 321–323. date_created: 2020-01-15T12:13:15Z date_published: 2019-02-20T00:00:00Z date_updated: 2021-01-12T08:12:45Z day: '20' doi: 10.1016/j.joule.2019.01.020 extern: '1' intvolume: ' 3' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.1016/j.joule.2019.01.020 month: '02' oa: 1 oa_version: Published Version page: 321-323 publication: Joule publication_identifier: issn: - 2542-4351 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Li-O2 cell-scale energy densities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2019' ... --- _id: '7358' abstract: - lang: eng text: Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSCs are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSCs compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily signaling pathways and increased expression of genes associated with naïve pluripotency. We further identify combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enable reproducible formation of brain structures suitable for disease modeling. article_processing_charge: No author: - first_name: Momoko full_name: Watanabe, Momoko last_name: Watanabe - first_name: Jillian R. full_name: Haney, Jillian R. last_name: Haney - first_name: Neda full_name: Vishlaghi, Neda last_name: Vishlaghi - first_name: Felix full_name: Turcios, Felix last_name: Turcios - first_name: Jessie E. full_name: Buth, Jessie E. last_name: Buth - first_name: Wen full_name: Gu, Wen last_name: Gu - first_name: Amanda J. full_name: Collier, Amanda J. last_name: Collier - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 - first_name: Di full_name: Chen, Di last_name: Chen - first_name: Shan full_name: Sabri, Shan last_name: Sabri - first_name: Amander T. full_name: Clark, Amander T. last_name: Clark - first_name: Kathrin full_name: Plath, Kathrin last_name: Plath - first_name: Heather R. full_name: Christofk, Heather R. last_name: Christofk - first_name: Michael J. full_name: Gandal, Michael J. last_name: Gandal - first_name: Bennett G. full_name: Novitch, Bennett G. last_name: Novitch citation: ama: Watanabe M, Haney JR, Vishlaghi N, et al. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. 2019. doi:10.1101/2019.12.13.875773 apa: Watanabe, M., Haney, J. R., Vishlaghi, N., Turcios, F., Buth, J. E., Gu, W., … Novitch, B. G. (2019). TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2019.12.13.875773 chicago: Watanabe, Momoko, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Jessie E. Buth, Wen Gu, Amanda J. Collier, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv. Cold Spring Harbor Laboratory, 2019. https://doi.org/10.1101/2019.12.13.875773. ieee: M. Watanabe et al., “TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids,” bioRxiv. Cold Spring Harbor Laboratory, 2019. ista: Watanabe M, Haney JR, Vishlaghi N, Turcios F, Buth JE, Gu W, Collier AJ, Miranda O, Chen D, Sabri S, Clark AT, Plath K, Christofk HR, Gandal MJ, Novitch BG. 2019. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv, 10.1101/2019.12.13.875773. mla: Watanabe, Momoko, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv, Cold Spring Harbor Laboratory, 2019, doi:10.1101/2019.12.13.875773. short: M. Watanabe, J.R. Haney, N. Vishlaghi, F. Turcios, J.E. Buth, W. Gu, A.J. Collier, O. Miranda, D. Chen, S. Sabri, A.T. Clark, K. Plath, H.R. Christofk, M.J. Gandal, B.G. Novitch, BioRxiv (2019). date_created: 2020-01-23T09:53:40Z date_published: 2019-12-13T00:00:00Z date_updated: 2022-06-17T08:03:32Z day: '13' doi: 10.1101/2019.12.13.875773 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2019.12.13.875773 month: '12' oa: 1 oa_version: Preprint page: '75' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7401' abstract: - lang: eng text: 'The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. ' alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kyncl, Jan last_name: Kyncl citation: ama: 'Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: 35th International Symposium on Computational Geometry (SoCG 2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39' apa: 'Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In 35th International Symposium on Computational Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39' chicago: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In 35th International Symposium on Computational Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39. ieee: R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in 35th International Symposium on Computational Geometry (SoCG 2019), Portland, OR, United States, 2019, vol. 129. ista: 'Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.' mla: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” 35th International Symposium on Computational Geometry (SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.SOCG.2019.39. short: R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2020-01-29T16:17:05Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:13:24Z day: '01' ddc: - '000' department: - _id: UlWa doi: 10.4230/LIPICS.SOCG.2019.39 external_id: arxiv: - '1903.08637' file: - access_level: open_access checksum: aac37b09118cc0ab58cf77129e691f8c content_type: application/pdf creator: dernst date_created: 2020-02-04T09:14:31Z date_updated: 2020-07-14T12:47:57Z file_id: '7445' file_name: 2019_LIPIcs_Fulek.pdf file_size: 628347 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: 35th International Symposium on Computational Geometry (SoCG 2019) publication_identifier: isbn: - 978-3-95977-104-7 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Z_2-Genus of graphs and minimum rank of partial symmetric matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '7453' abstract: - lang: eng text: We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO. alternative_title: - Lecture Notes in Computer Science article_processing_charge: No author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Kim G. full_name: Larsen, Kim G. last_name: Larsen - first_name: Marius full_name: Mikučionis, Marius last_name: Mikučionis citation: ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22' apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen & G. Woeginger (Eds.), Computing and Software Science (Vol. 10000, pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22 chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22. ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in Computing and Software Science, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477. ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.' mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22. short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477. date_created: 2020-02-05T10:51:44Z date_published: 2019-10-05T00:00:00Z date_updated: 2022-09-06T08:25:52Z day: '05' department: - _id: ToHe doi: 10.1007/978-3-319-91908-9_22 editor: - first_name: Bernhard full_name: Steffen, Bernhard last_name: Steffen - first_name: Gerhard full_name: Woeginger, Gerhard last_name: Woeginger intvolume: ' 10000' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-319-91908-9_22 month: '10' oa: 1 oa_version: Published Version page: 452-477 project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computing and Software Science publication_identifier: eisbn: - '9783319919089' eissn: - 0302-9743 isbn: - '9783319919072' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Continuous-time models for system design and analysis type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10000 year: '2019' ... --- _id: '7459' abstract: - lang: eng text: We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the hydrothermal transformation of TiO2 have both inner and outer surfaces, which facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The magnetoelectric coupling was studied by measuring the piezoelectric behavior in the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly on Ti substrate may lead to efficient fabrication of magnetoelectric devices. article_processing_charge: No article_type: original author: - first_name: Samba Siva full_name: Vadla, Samba Siva last_name: Vadla - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Subish full_name: John, Subish last_name: John - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu - first_name: Somnath C. full_name: Roy, Somnath C. last_name: Roy citation: ama: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 2019;159:33-36. doi:10.1016/j.scriptamat.2018.09.003 apa: Vadla, S. S., Costanzo, T., John, S., Caruntu, G., & Roy, S. C. (2019). Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. Elsevier. https://doi.org/10.1016/j.scriptamat.2018.09.003 chicago: Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” Scripta Materialia. Elsevier, 2019. https://doi.org/10.1016/j.scriptamat.2018.09.003. ieee: S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” Scripta Materialia, vol. 159. Elsevier, pp. 33–36, 2019. ista: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36. mla: Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” Scripta Materialia, vol. 159, Elsevier, 2019, pp. 33–36, doi:10.1016/j.scriptamat.2018.09.003. short: S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia 159 (2019) 33–36. date_created: 2020-02-05T14:19:17Z date_published: 2019-01-15T00:00:00Z date_updated: 2023-02-23T13:08:31Z day: '15' doi: 10.1016/j.scriptamat.2018.09.003 extern: '1' intvolume: ' 159' language: - iso: eng month: '01' oa_version: None page: 33-36 publication: Scripta Materialia publication_identifier: issn: - 1359-6462 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2019' ... --- _id: '7476' abstract: - lang: eng text: The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent maintenance remain poorly understood. Here, we apply large-scale quantitative fate mapping to define the patterns of cell fate behaviour during SG development and maintenance. We show that the SG develops from a defined number of lineage-restricted progenitors that undergo a programme of independent and stochastic cell fate decisions. Following an expansion phase, equipotent progenitors transition into a phase of homeostatic turnover, which is correlated with changes in the mechanical properties of the stroma and spatial restrictions on gland size. Expression of the oncogene KrasG12D results in a release from these constraints and unbridled gland expansion. Quantitative clonal fate analysis reveals that, during this phase, the primary effect of the Kras oncogene is to drive a constant fate bias with little effect on cell division rates. These findings provide insight into the developmental programme of the SG, as well as the mechanisms that drive tumour progression and gland dysfunction. article_processing_charge: No article_type: original author: - first_name: Marianne Stemann full_name: Andersen, Marianne Stemann last_name: Andersen - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Svetlana full_name: Ulyanchenko, Svetlana last_name: Ulyanchenko - first_name: Soline full_name: Estrach, Soline last_name: Estrach - first_name: Yasuko full_name: Antoku, Yasuko last_name: Antoku - first_name: Sabrina full_name: Pisano, Sabrina last_name: Pisano - first_name: Kim E. full_name: Boonekamp, Kim E. last_name: Boonekamp - first_name: Sarah full_name: Sendrup, Sarah last_name: Sendrup - first_name: Martti full_name: Maimets, Martti last_name: Maimets - first_name: Marianne Terndrup full_name: Pedersen, Marianne Terndrup last_name: Pedersen - first_name: Jens V. full_name: Johansen, Jens V. last_name: Johansen - first_name: Ditte L. full_name: Clement, Ditte L. last_name: Clement - first_name: Chloe C. full_name: Feral, Chloe C. last_name: Feral - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Kim B. full_name: Jensen, Kim B. last_name: Jensen citation: ama: Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 2019;21(8):924-932. doi:10.1038/s41556-019-0362-x apa: Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y., Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0362-x chicago: Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0362-x. ieee: M. S. Andersen et al., “Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states,” Nature Cell Biology, vol. 21, no. 8. Springer Nature, pp. 924–932, 2019. ista: Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 21(8), 924–932. mla: Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” Nature Cell Biology, vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:10.1038/s41556-019-0362-x. short: M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano, K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement, C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932. date_created: 2020-02-11T08:43:49Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:13:47Z day: '01' doi: 10.1038/s41556-019-0362-x extern: '1' external_id: pmid: - '31358966' intvolume: ' 21' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/ month: '08' oa: 1 oa_version: Submitted Version page: 924-932 pmid: 1 publication: Nature Cell Biology publication_identifier: issn: - 1465-7392 - 1476-4679 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2019' ... --- _id: '7548' abstract: - lang: eng text: Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity. article_number: e0217746 article_processing_charge: No article_type: original author: - first_name: Tessa full_name: Sinnige, Tessa last_name: Sinnige - first_name: Prashanth full_name: Ciryam, Prashanth last_name: Ciryam - first_name: Samuel full_name: Casford, Samuel last_name: Casford - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo citation: ama: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 2019;14(5). doi:10.1371/journal.pone.0217746 apa: Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., & Vendruscolo, M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0217746 chicago: Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson, Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0217746. ieee: T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo, “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response,” PLOS ONE, vol. 14, no. 5. Public Library of Science, 2019. ista: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 14(5), e0217746. mla: Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” PLOS ONE, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:10.1371/journal.pone.0217746. short: T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo, PLOS ONE 14 (2019). date_created: 2020-02-28T10:45:13Z date_published: 2019-05-31T00:00:00Z date_updated: 2021-01-12T08:14:08Z day: '31' doi: 10.1371/journal.pone.0217746 extern: '1' intvolume: ' 14' issue: '5' language: - iso: eng month: '05' oa_version: Published Version publication: PLOS ONE publication_identifier: issn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2019' ... --- _id: '7547' abstract: - lang: eng text: The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms. article_processing_charge: No article_type: original author: - first_name: Jesse full_name: Cohn, Jesse last_name: Cohn - first_name: Vivek full_name: Dwivedi, Vivek last_name: Dwivedi - first_name: Giulio full_name: Valperga, Giulio last_name: Valperga - first_name: Nicole full_name: Zarate, Nicole last_name: Zarate - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: H. Robert full_name: Horvitz, H. Robert last_name: Horvitz - first_name: Jonathan T. full_name: Pierce, Jonathan T. last_name: Pierce citation: ama: 'Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 2019;9(11):3703-3714. doi:10.1534/g3.119.400654' apa: 'Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., & Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.119.400654' chicago: 'Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono, H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/g3.119.400654.' ieee: 'J. Cohn et al., “Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” G3: Genes, Genomes, Genetics, vol. 9, no. 11. Genetics Society of America, pp. 3703–3714, 2019.' ista: 'Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. 2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 9(11), 3703–3714.' mla: 'Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes, Genetics, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14, doi:10.1534/g3.119.400654.' short: 'J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T. Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.' date_created: 2020-02-28T10:44:27Z date_published: 2019-11-01T00:00:00Z date_updated: 2021-01-12T08:14:07Z day: '01' doi: 10.1534/g3.119.400654 extern: '1' external_id: pmid: - '31519744' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa_version: Published Version page: 3703-3714 pmid: 1 publication: 'G3: Genes, Genomes, Genetics' publication_identifier: issn: - 2160-1836 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2019' ... --- _id: '7550' abstract: - lang: eng text: 'We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ' acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375. article_processing_charge: No article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Ulisse full_name: Stefanelli, Ulisse last_name: Stefanelli citation: ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 2019;28(2):425-447. apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. Gakko Tosho. chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications. Gakko Tosho, 2019. ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” Advances in Mathematical Sciences and Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019. ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447. mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47. short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447. date_created: 2020-02-28T10:54:41Z date_published: 2019-10-22T00:00:00Z date_updated: 2022-06-17T07:52:41Z day: '22' department: - _id: JaMa external_id: arxiv: - '1910.10050' intvolume: ' 28' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1910.10050' month: '10' oa: 1 oa_version: Preprint page: 425-447 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Advances in Mathematical Sciences and Applications publication_identifier: issn: - 1343-4373 publication_status: published publisher: Gakko Tosho quality_controlled: '1' status: public title: Penalization via global functionals of optimal-control problems for dissipative evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2019' ... --- _id: '7552' abstract: - lang: eng text: 'There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ' article_processing_charge: No author: - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579. apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv. chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d. ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv. ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, . mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv. short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.). date_created: 2020-02-28T10:57:08Z date_published: 2019-12-18T00:00:00Z date_updated: 2021-01-12T08:14:09Z day: '18' department: - _id: GaTk external_id: arxiv: - '1912.08579' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.08579 month: '12' oa: 1 oa_version: Preprint page: '5' project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: arXiv:1912.08579 publication_status: submitted publisher: ArXiv status: public title: Action at a distance in transcriptional regulation type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7576' abstract: - lang: eng text: We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools. article_processing_charge: No author: - first_name: Fabian full_name: Immler, Fabian last_name: Immler - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff - first_name: Luis full_name: Benet, Luis last_name: Benet - first_name: Alexandre full_name: Chapoutot, Alexandre last_name: Chapoutot - first_name: Xin full_name: Chen, Xin last_name: Chen - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Luca full_name: Geretti, Luca last_name: Geretti - first_name: Niklas full_name: Kochdumper, Niklas last_name: Kochdumper - first_name: David P. full_name: Sanders, David P. last_name: Sanders - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b' apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b' chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.' ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.' ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.' mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b.' short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61. conference: end_date: 2019-04-15 location: Montreal, Canada name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems' start_date: 2019-04-15 date_created: 2020-03-08T23:00:49Z date_published: 2019-05-25T00:00:00Z date_updated: 2021-01-12T08:14:17Z day: '25' ddc: - '000' department: - _id: ToHe doi: 10.29007/m75b file: - access_level: open_access checksum: 9138977a06fcd6a95976eb4bca875f0c content_type: application/pdf creator: dernst date_created: 2020-03-24T07:36:36Z date_updated: 2020-07-14T12:48:00Z file_id: '7617' file_name: 2019_ARCH19_Immler.pdf file_size: 1934830 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 61' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 41-61 publication: EPiC Series in Computing publication_identifier: eissn: - '23987340' publication_status: published publisher: EasyChair Publications quality_controlled: '1' scopus_import: 1 status: public title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '7627' abstract: - lang: eng text: 'Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and beyond. ' article_processing_charge: No author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: Manfred full_name: Nachtnebel, Manfred last_name: Nachtnebel - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. apa: Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. ChemRxiv. chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv, n.d. ieee: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S. A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.” ChemRxiv. ista: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. mla: Prehal, Christian, et al. A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering. ChemRxiv. short: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, (n.d.). date_created: 2020-04-01T10:10:21Z date_published: 2019-12-26T00:00:00Z date_updated: 2020-04-06T10:36:21Z day: '26' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv.11447775.v1 month: '12' oa: 1 oa_version: Preprint page: '50' publication_status: submitted publisher: ChemRxiv status: public title: A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7710' abstract: - lang: eng text: 'The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.' article_number: '5436' article_processing_charge: No article_type: original author: - first_name: Olivier full_name: Delaneau, Olivier last_name: Delaneau - first_name: Jean-François full_name: Zagury, Jean-François last_name: Zagury - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Jonathan L. full_name: Marchini, Jonathan L. last_name: Marchini - first_name: Emmanouil T. full_name: Dermitzakis, Emmanouil T. last_name: Dermitzakis citation: ama: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nature Communications. 2019;10. doi:10.1038/s41467-019-13225-y apa: Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y chicago: Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y. ieee: O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436. mla: Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y. short: O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019). date_created: 2020-04-30T10:40:32Z date_published: 2019-11-28T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '28' doi: 10.1038/s41467-019-13225-y extern: '1' intvolume: ' 10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-019-13225-y month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Accurate, scalable and integrative haplotype estimation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '7711' abstract: - lang: eng text: The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies. article_processing_charge: No article_type: original author: - first_name: Roel P. J. full_name: Bevers, Roel P. J. last_name: Bevers - first_name: Maria full_name: Litovchenko, Maria last_name: Litovchenko - first_name: Adamandia full_name: Kapopoulou, Adamandia last_name: Kapopoulou - first_name: Virginie S. full_name: Braman, Virginie S. last_name: Braman - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Johan full_name: Auwerx, Johan last_name: Auwerx - first_name: Brian full_name: Hollis, Brian last_name: Hollis - first_name: Bart full_name: Deplancke, Bart last_name: Deplancke citation: ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3 apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3 chicago: Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3. ieee: R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019. ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242. mla: Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3. short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242. date_created: 2020-04-30T10:40:56Z date_published: 2019-12-09T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '09' doi: 10.1038/s42255-019-0147-3 extern: '1' intvolume: ' 1' issue: '12' language: - iso: eng month: '12' oa_version: None page: 1226-1242 publication: Nature Metabolism publication_identifier: issn: - 2522-5812 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s42255-020-0202-0 status: public title: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2019' ... --- _id: '7782' abstract: - lang: eng text: As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures. article_processing_charge: No author: - first_name: Jonathan full_name: Sulc, Jonathan last_name: Sulc - first_name: Ninon full_name: Mounier, Ninon last_name: Mounier - first_name: Felix full_name: Günther, Felix last_name: Günther - first_name: Thomas full_name: Winkler, Thomas last_name: Winkler - first_name: Andrew R. full_name: Wood, Andrew R. last_name: Wood - first_name: Timothy M. full_name: Frayling, Timothy M. last_name: Frayling - first_name: Iris M. full_name: Heid, Iris M. last_name: Heid - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Zoltán full_name: Kutalik, Zoltán last_name: Kutalik citation: ama: 'Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019.' apa: 'Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.' chicago: 'Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.' ieee: 'J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.' ista: 'Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .' mla: 'Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.' short: J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019). date_created: 2020-04-30T13:04:26Z date_published: 2019-06-14T00:00:00Z date_updated: 2021-01-12T08:15:30Z day: '14' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/632380 ' month: '06' oa: 1 oa_version: Preprint page: '20' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: 'Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8013' article_number: e1007049 article_processing_charge: No article_type: original author: - first_name: Christopher B. full_name: Currin, Christopher B. last_name: Currin - first_name: Phumlani N. full_name: Khoza, Phumlani N. last_name: Khoza - first_name: Alexander D. full_name: Antrobus, Alexander D. last_name: Antrobus - first_name: Peter E. full_name: Latham, Peter E. last_name: Latham - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Joseph V. full_name: Raimondo, Joseph V. last_name: Raimondo citation: ama: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049' apa: 'Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049' chicago: 'Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.' ieee: 'C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.' ista: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.' mla: 'Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.' short: C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019). date_created: 2020-06-25T12:50:39Z date_published: 2019-07-11T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '11' ddc: - '570' doi: 10.1371/journal.pcbi.1007049 extern: '1' external_id: pmid: - '31295253' file: - access_level: open_access checksum: 723bdfb6ee5c747cbbb32baf01d17fad content_type: application/pdf creator: cziletti date_created: 2020-07-02T12:22:57Z date_updated: 2020-07-14T12:48:08Z file_id: '8079' file_name: 2019_PlosCompBio_Currin.pdf file_size: 773969 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 15' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: 'Think: Theory for Africa' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 15 year: '2019' ... --- _id: '8014' abstract: - lang: eng text: 'Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework.' article_processing_charge: No article_type: original author: - first_name: Sanjay G. full_name: Manohar, Sanjay G. last_name: Manohar - first_name: Nahid full_name: Zokaei, Nahid last_name: Zokaei - first_name: Sean J. full_name: Fallon, Sean J. last_name: Fallon - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Masud full_name: Husain, Masud last_name: Husain citation: ama: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017 apa: Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017 chicago: Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017. ieee: S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019. ista: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12. mla: Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017. short: S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12. date_created: 2020-06-25T12:52:13Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '01' ddc: - '570' doi: 10.1016/j.neubiorev.2019.03.017 extern: '1' external_id: pmid: - '30922977' file: - access_level: open_access checksum: 7b972e3d6f7bb3122c8c5648f44e60ca content_type: application/pdf creator: cziletti date_created: 2020-07-02T13:17:52Z date_updated: 2020-07-14T12:48:08Z file_id: '8080' file_name: 2019_NeurosBiobehavRev_Manohar.pdf file_size: 1754418 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 101' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/233007 ' month: '06' oa: 1 oa_version: Published Version page: 1-12 pmid: 1 publication: Neuroscience and Biobehavioral Reviews publication_identifier: issn: - 0149-7634 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Neural mechanisms of attending to items in working memory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 101 year: '2019' ... --- _id: '8175' abstract: - lang: eng text: We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices. acknowledgement: "D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n" article_number: '34' article_processing_charge: No author: - first_name: Dan full_name: Betea, Dan last_name: Betea - first_name: Jérémie full_name: Bouttier, Jérémie last_name: Bouttier - first_name: Peter full_name: Nejjar, Peter id: 4BF426E2-F248-11E8-B48F-1D18A9856A87 last_name: Nejjar - first_name: Mirjana full_name: Vuletíc, Mirjana last_name: Vuletíc citation: ama: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.' apa: 'Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.' chicago: Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019. ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019. ista: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.' mla: Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019. short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019. conference: end_date: 2019-07-05 location: Ljubljana, Slovenia name: 'FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics' start_date: 2019-07-01 date_created: 2020-07-26T22:01:04Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:17:18Z day: '01' department: - _id: LaEr ec_funded: 1 external_id: arxiv: - '1902.08750' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.08750 month: '07' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics publication_status: published publisher: Formal Power Series and Algebraic Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: New edge asymptotics of skew Young diagrams via free boundaries type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8228' abstract: - lang: eng text: "Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge." article_number: '100044' article_processing_charge: No article_type: original author: - first_name: Josef full_name: Singer, Josef last_name: Singer orcid: 0000-0002-8701-2412 - first_name: Gertrude full_name: Achatz-Straussberger, Gertrude last_name: Achatz-Straussberger - first_name: Anna full_name: Bentley-Lukschal, Anna last_name: Bentley-Lukschal - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Gernot full_name: Achatz, Gernot last_name: Achatz - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044' apa: 'Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044' chicago: 'Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.' ieee: 'J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.' ista: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.' mla: 'Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.' short: J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019). date_created: 2020-08-10T11:50:54Z date_published: 2019-07-29T00:00:00Z date_updated: 2021-01-12T08:17:36Z day: '29' doi: 10.1016/j.waojou.2019.100044 extern: '1' intvolume: ' 12' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.waojou.2019.100044 month: '07' oa: 1 oa_version: Published Version publication: World Allergy Organization Journal publication_identifier: issn: - 1939-4551 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '8229' abstract: - lang: eng text: Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response. article_number: '2463' article_processing_charge: No article_type: original author: - first_name: Anna S. full_name: Ondracek, Anna S. last_name: Ondracek orcid: 0000-0001-7625-3651 - first_name: Denise full_name: Heiden, Denise last_name: Heiden - first_name: Gertie J. full_name: Oostingh, Gertie J. last_name: Oostingh - first_name: Elisabeth full_name: Fuerst, Elisabeth last_name: Fuerst - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Cornelia full_name: Bergmayr, Cornelia last_name: Bergmayr - first_name: Johanna full_name: Rohrhofer, Johanna last_name: Rohrhofer orcid: 0000-0002-2783-2099 - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim orcid: 0000-0003-4019-5765 - first_name: Albert full_name: Duschl, Albert last_name: Duschl orcid: 0000-0002-7034-9860 - first_name: Eva full_name: Untersmayr, Eva last_name: Untersmayr orcid: 0000-0002-1963-499X citation: ama: Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463 apa: Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463 chicago: Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463. ieee: A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019. ista: Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463. mla: Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463. short: A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019). date_created: 2020-08-10T11:51:04Z date_published: 2019-10-15T00:00:00Z date_updated: 2021-01-12T08:17:36Z day: '15' doi: 10.3390/nu11102463 extern: '1' intvolume: ' 11' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3390/nu11102463 month: '10' oa: 1 oa_version: Published Version publication: Nutrients publication_identifier: issn: - 2072-6643 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2019' ... --- _id: '8227' article_processing_charge: No article_type: letter_note author: - first_name: Kristina M. full_name: Ilieva, Kristina M. last_name: Ilieva - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Heather J. full_name: Bax, Heather J. last_name: Bax - first_name: Silvia full_name: Crescioli, Silvia last_name: Crescioli - first_name: Laura full_name: Montero‐Morales, Laura last_name: Montero‐Morales - first_name: Silvia full_name: Mele, Silvia last_name: Mele - first_name: Heng Sheng full_name: Sow, Heng Sheng last_name: Sow - first_name: Chara full_name: Stavraka, Chara last_name: Stavraka - first_name: Debra H. full_name: Josephs, Debra H. last_name: Josephs - first_name: James F. full_name: Spicer, James F. last_name: Spicer - first_name: Herta full_name: Steinkellner, Herta last_name: Steinkellner orcid: 0000-0003-4823-1505 - first_name: Erika full_name: Jensen‐Jarolim, Erika last_name: Jensen‐Jarolim orcid: 0000-0003-4019-5765 - first_name: Andrew N. J. full_name: Tutt, Andrew N. J. last_name: Tutt orcid: 0000-0001-8715-2901 - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis orcid: 0000-0002-4100-7810 citation: ama: 'Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818' apa: 'Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818' chicago: 'Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.' ieee: 'K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.' ista: 'Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.' mla: 'Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.' short: K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989. date_created: 2020-08-10T11:50:42Z date_published: 2019-10-01T00:00:00Z date_updated: 2021-01-12T08:17:35Z day: '01' doi: 10.1111/all.13818 extern: '1' intvolume: ' 74' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/all.13818 month: '10' oa: 1 oa_version: Published Version page: 1985-1989 publication: Allergy publication_identifier: issn: - 0105-4538 - 1398-9995 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2019' ... --- _id: '8263' abstract: - lang: eng text: "Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines." article_number: '83' article_processing_charge: No article_type: original author: - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin orcid: 0000-0003-0120-9319 - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Anna A. full_name: Karan, Anna A. last_name: Karan - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6' apa: 'Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6' chicago: 'Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6.' ieee: 'P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.' ista: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.' mla: 'Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.' short: P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019). date_created: 2020-08-15T11:04:07Z date_published: 2019-03-27T00:00:00Z date_updated: 2023-02-23T13:28:54Z day: '27' doi: 10.1186/s12862-019-1403-6 extern: '1' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s12862-019-1403-6 month: '03' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_identifier: issn: - 1471-2148 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '8296' abstract: - lang: eng text: While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting. article_processing_charge: No author: - first_name: Enis Ceyhun full_name: Alp, Enis Ceyhun last_name: Alp - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Georgia full_name: Fragkouli, Georgia last_name: Fragkouli - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448' apa: 'Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448' chicago: Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448. ieee: E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112. ista: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.' mla: Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448. short: E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112. conference: end_date: 2019-05-15 location: Bertinoro, Italy name: 'HotOS: Workshop on Hot Topics in Operating Systems' start_date: 2019-05-13 date_created: 2020-08-26T11:45:45Z date_published: 2019-05-01T00:00:00Z date_updated: 2021-01-12T08:17:56Z day: '01' doi: 10.1145/3317550.3321448 extern: '1' language: - iso: eng month: '05' oa_version: None page: 105-112 publication: Proceedings of the Workshop on Hot Topics in Operating Systems publication_identifier: isbn: - '9781450367271' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Rethinking general-purpose decentralized computing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8304' abstract: - lang: eng text: "Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field." article_number: 2019/1128 article_processing_charge: No author: - first_name: Alexei full_name: Zamyatin, Alexei last_name: Zamyatin - first_name: Mustafa full_name: Al-Bassam, Mustafa last_name: Al-Bassam - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Pedro full_name: Moreno-Sanchez, Pedro last_name: Moreno-Sanchez - first_name: Aggelos full_name: Kiayias, Aggelos last_name: Kiayias - first_name: William J. full_name: Knottenbelt, William J. last_name: Knottenbelt citation: ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.' apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive.' chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.' ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .' ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.' mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.' short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.). date_created: 2020-08-26T12:16:38Z date_published: 2019-10-01T00:00:00Z date_updated: 2021-09-24T12:08:14Z day: '01' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://eprint.iacr.org/2019/1128 ' month: '10' oa: 1 oa_version: Preprint publication: Cryptology ePrint Archive publication_status: submitted status: public title: 'SoK: Communication across distributed ledgers' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8303' abstract: - lang: eng text: 'ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin.' article_number: 2019/676 article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive. apa: Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive. chicago: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d. ieee: E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. . ista: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676. mla: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676. short: E. Kokoris Kogias, Cryptology EPrint Archive (n.d.). date_created: 2020-08-26T12:13:56Z date_published: 2019-06-06T00:00:00Z date_updated: 2021-09-24T12:07:11Z day: '06' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/676 month: '06' oa: 1 oa_version: Preprint publication: Cryptology ePrint Archive publication_status: submitted status: public title: Robust and scalable consensus for sharded distributed ledgers type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8311' abstract: - lang: eng text: 'One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope.' article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101 apa: Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101 chicago: Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101. ieee: E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019. ista: Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. mla: Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101. short: E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019. date_created: 2020-08-27T11:22:24Z date_published: 2019-09-27T00:00:00Z date_updated: 2021-12-20T15:30:47Z day: '27' degree_awarded: PhD doi: 10.5075/epfl-thesis-7101 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.5075/epfl-thesis-7101 month: '09' oa: 1 oa_version: Published Version page: '244' publication_status: published publisher: École Polytechnique Fédérale de Lausanne status: public supervisor: - first_name: Bryan Alexander full_name: Ford, Bryan Alexander last_name: Ford title: Secure, confidential blockchains providing high throughput and low latency type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8314' abstract: - lang: eng text: "Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called Wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee's approval for the last valid state. Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. Furthermore, we consider permissioned blockchains, where the additional property of auditability might be desired for regulatory purposes. We introduce Brick+, an off-chain construction that provides auditability on top of Brick without conflicting with its privacy guarantees. We formally define the properties our payment channel construction should fulfill, and prove that both Brick and Brick+ satisfy them. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity." article_number: '1905.11360' article_processing_charge: No author: - first_name: Georgia full_name: Avarikioti, Georgia last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros citation: ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv.' apa: 'Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.). Brick: Asynchronous payment channels. arXiv.' chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.' ieee: 'G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” arXiv. .' ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.' mla: 'Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv, 1905.11360.' short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.). date_created: 2020-08-27T11:36:54Z date_published: 2019-05-27T00:00:00Z date_updated: 2021-01-12T08:18:04Z day: '27' extern: '1' external_id: arxiv: - '1905.11360' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.11360 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Brick: Asynchronous payment channels' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8315' abstract: - lang: eng text: "Sharding distributed ledgers is the most promising on-chain solution for scaling blockchain technology. In this work, we define and analyze the properties a sharded distributed ledger should fulfill. More specifically, we show that a sharded blockchain cannot be scalable under a fully adaptive adversary, but it can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible only if the distributed ledger creates succinct proofs of the valid state updates at the end of each epoch. Our model builds upon and extends the Bitcoin backbone protocol by defining consistency and\r\nscalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system. In\r\norder to show the power of our framework, we analyze the most prominent sharded blockchains and either prove their correctness (OmniLedger, RapidChain) under our model or pinpoint where they fail to balance the consistency and\r\nscalability requirements (Elastico, Monoxide). " article_number: '1910.10434' article_processing_charge: No author: - first_name: Georgia full_name: Avarikioti, Georgia last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer citation: ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.' apa: 'Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.' chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, n.d.' ieee: 'G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” arXiv. .' ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.' mla: 'Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, 1910.10434.' short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.). date_created: 2020-08-27T11:37:43Z date_published: 2019-10-23T00:00:00Z date_updated: 2021-01-12T08:18:05Z day: '23' extern: '1' external_id: arxiv: - '1910.10434' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.10434 month: '10' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Divide and scale: Formalization of distributed ledger sharding protocols' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8313' abstract: - lang: eng text: The present invention concerns a computer-implemented method for secure data exchange between a sender (A) and a recipient (B), wherein the method is performed by the sender (A) and comprises encrypting data using a symmetric key k, creating a write transaction T W , wherein the write transaction T W comprises information usable to derive the symmetric key k and an access policy identifying the recipient (B) as being allowed to decrypt the encrypted data, providing the recipient (B) access to the encrypted data, and sending the write transaction T W to a first group of servers (AC) for being stored in a blockchain data structure maintained by the first group of servers (AC). applicant: - 'École Polytechnique Fédérale De Lausanne ' article_processing_charge: No author: - first_name: Bryan full_name: Ford, Bryan last_name: Ford - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Janovic, Philipp last_name: Janovic citation: ama: Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019. apa: Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods and systems for secure data exchange. chicago: Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “Methods and Systems for Secure Data Exchange,” 2019. ieee: B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019. ista: Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for secure data exchange. mla: Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019. short: B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019). date_created: 2020-08-27T11:24:44Z date_published: 2019-08-22T00:00:00Z date_updated: 2022-01-05T14:00:32Z day: '22' extern: '1' ipc: G06F21/62 ; H04L9/08 ; H04L9/32 ipn: WO2019158209 (A1) main_file_link: - open_access: '1' url: https://patents.google.com/patent/WO2019158209A1 month: '08' oa: 1 oa_version: Published Version publication_date: 2019-08-22 status: public title: Methods and systems for secure data exchange type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8405' abstract: - lang: eng text: Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available. article_number: '2697' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Leandro F. full_name: Estrozi, Leandro F. last_name: Estrozi - first_name: Charles D. full_name: Schwieters, Charles D. last_name: Schwieters - first_name: Gregory full_name: Effantin, Gregory last_name: Effantin - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Remy full_name: Sounier, Remy last_name: Sounier - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Elena full_name: Schmidt, Elena last_name: Schmidt - first_name: Rime full_name: Kerfah, Rime last_name: Kerfah - first_name: Guillaume full_name: Mas, Guillaume last_name: Mas - first_name: Jacques-Philippe full_name: Colletier, Jacques-Philippe last_name: Colletier - first_name: Peter full_name: Güntert, Peter last_name: Güntert - first_name: Adrien full_name: Favier, Adrien last_name: Favier - first_name: Guy full_name: Schoehn, Guy last_name: Schoehn - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Jerome full_name: Boisbouvier, Jerome last_name: Boisbouvier citation: ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9 apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9 chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9. ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697. mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9. short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019). date_created: 2020-09-17T10:28:25Z date_published: 2019-06-19T00:00:00Z date_updated: 2021-01-12T08:19:03Z day: '19' doi: 10.1038/s41467-019-10490-9 extern: '1' external_id: pmid: - '31217444' intvolume: ' 10' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-019-10490-9 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '8406' abstract: - lang: eng text: Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation. article_number: eaaw3818 article_processing_charge: No article_type: original author: - first_name: Jan full_name: Felix, Jan last_name: Felix - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Cecile full_name: Morlot, Cecile last_name: Morlot - first_name: Olga full_name: Abian, Olga last_name: Abian - first_name: Irina full_name: Gutsche, Irina last_name: Gutsche - first_name: Adrian full_name: Velazquez-Campoy, Adrian last_name: Velazquez-Campoy - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga citation: ama: Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818 apa: Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818 chicago: Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818. ieee: J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019. ista: Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818. mla: Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818. short: J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019). date_created: 2020-09-17T10:28:36Z date_published: 2019-09-04T00:00:00Z date_updated: 2021-01-12T08:19:03Z day: '04' doi: 10.1126/sciadv.aaw3818 extern: '1' intvolume: ' 5' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1126/sciadv.aaw3818' month: '09' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2019' ... --- _id: '8413' abstract: - lang: eng text: NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains. article_processing_charge: No article_type: original author: - first_name: Petra full_name: Rovó, Petra last_name: Rovó - first_name: Colin A. full_name: Smith, Colin A. last_name: Smith - first_name: Diego full_name: Gauto, Diego last_name: Gauto - first_name: Bert L. full_name: de Groot, Bert L. last_name: de Groot - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Rasmus full_name: Linser, Rasmus last_name: Linser citation: ama: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258 apa: Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258 chicago: Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258. ieee: P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019. ista: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869. mla: Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258. short: P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869. date_created: 2020-09-17T10:29:50Z date_published: 2019-01-08T00:00:00Z date_updated: 2021-01-12T08:19:07Z day: '08' doi: 10.1021/jacs.8b09258 extern: '1' external_id: pmid: - '30620186' intvolume: ' 141' issue: '2' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '01' oa_version: Submitted Version page: 858-869 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2019' ... --- _id: '8412' abstract: - lang: eng text: Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid. article_processing_charge: No article_type: original author: - first_name: Matthew D. full_name: Shannon, Matthew D. last_name: Shannon - first_name: Theint full_name: Theint, Theint last_name: Theint - first_name: Dwaipayan full_name: Mukhopadhyay, Dwaipayan last_name: Mukhopadhyay - first_name: Krystyna full_name: Surewicz, Krystyna last_name: Surewicz - first_name: Witold K. full_name: Surewicz, Witold K. last_name: Surewicz - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Christopher P. full_name: Jaroniec, Christopher P. last_name: Jaroniec citation: ama: Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779 apa: Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779 chicago: Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779. ieee: M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019. ista: Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317. mla: Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779. short: M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317. date_created: 2020-09-17T10:29:43Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:06Z day: '21' doi: 10.1002/cphc.201800779 extern: '1' external_id: pmid: - '30276945' intvolume: ' 20' issue: '2' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '01' oa_version: Submitted Version page: 311-317 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '8411' abstract: - lang: eng text: 'Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.' article_processing_charge: No article_type: original author: - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Karine full_name: Giandoreggio-Barranco, Karine last_name: Giandoreggio-Barranco - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935 apa: Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935 chicago: Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935. ieee: D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019. ista: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284. mla: Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935. short: D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284. date_created: 2020-09-17T10:29:36Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:06Z day: '21' doi: 10.1002/cphc.201800935 extern: '1' external_id: pmid: - '30444575' intvolume: ' 20' issue: '2' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '01' oa_version: Submitted Version page: 276-284 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '8415' abstract: - lang: eng text: 'We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.' article_processing_charge: No article_type: original author: - first_name: Péter full_name: Bálint, Péter last_name: Bálint - first_name: Jacopo full_name: De Simoi, Jacopo last_name: De Simoi - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Martin full_name: Leguil, Martin last_name: Leguil citation: ama: Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x apa: Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x chicago: Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x. ieee: P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019. ista: Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575. mla: Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x. short: P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575. date_created: 2020-09-17T10:41:27Z date_published: 2019-05-09T00:00:00Z date_updated: 2021-01-12T08:19:08Z day: '09' doi: 10.1007/s00220-019-03448-x extern: '1' external_id: arxiv: - '1809.08947' intvolume: ' 374' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.08947 month: '05' oa: 1 oa_version: Preprint page: 1531-1575 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 374 year: '2019' ... --- _id: '8409' abstract: - lang: eng text: The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling. article_processing_charge: No article_type: original author: - first_name: Catherine full_name: Bougault, Catherine last_name: Bougault - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Waldemar full_name: Vollmer, Waldemar last_name: Vollmer - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009 apa: Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009 chicago: Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009. ieee: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019. ista: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72. mla: Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009. short: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72. date_created: 2020-09-17T10:29:10Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T08:19:05Z day: '01' doi: 10.1016/j.jsb.2018.07.009 extern: '1' external_id: pmid: - '30031884' intvolume: ' 206' issue: '1' keyword: - Structural Biology language: - iso: eng month: '04' oa_version: Submitted Version page: 66-72 pmid: 1 publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 206 year: '2019' ... --- _id: '8407' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025 apa: Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025 chicago: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025. ieee: P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019. ista: Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186. mla: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025. short: P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186. date_created: 2020-09-17T10:28:47Z date_published: 2019-09-01T00:00:00Z date_updated: 2021-01-12T08:19:04Z day: '01' doi: 10.1016/j.jmr.2019.07.025 extern: '1' external_id: pmid: - '31350165' intvolume: ' 306' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '09' oa_version: Submitted Version page: 180-186 pmid: 1 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Relaxing with liquids and solids – A perspective on biomolecular dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 306 year: '2019' ... --- _id: '8410' article_processing_charge: No article_type: letter_note author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Eduard Y. full_name: Chekmenev, Eduard Y. last_name: Chekmenev citation: ama: Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177. doi:10.1002/cphc.201801100 apa: Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201801100 chicago: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201801100. ieee: P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 177–177, 2019. ista: Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177. mla: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100. short: P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177. date_created: 2020-09-17T10:29:26Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:05Z day: '21' doi: 10.1002/cphc.201801100 extern: '1' external_id: pmid: - '30556633' intvolume: ' 20' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/cphc.201801100 month: '01' oa: 1 oa_version: Published Version page: 177-177 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: NMR for Biological Systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ...