[{"quality_controlled":"1","author":[{"last_name":"Sun","full_name":"Sun, Wendy Q.","first_name":"Wendy Q."},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"last_name":"De Graaff","first_name":"Anna","full_name":"De Graaff, Anna"},{"last_name":"Chisholm","first_name":"John","full_name":"Chisholm, John"},{"last_name":"Greene","full_name":"Greene, Jenny E.","first_name":"Jenny E."},{"last_name":"Oesch","full_name":"Oesch, Pascal A.","first_name":"Pascal A."},{"id":"018f0249-0e87-11f0-b167-cbce08fbd541","full_name":"Torralba Torregrosa, Alberto","first_name":"Alberto","last_name":"Torralba Torregrosa","orcid":"0000-0001-5586-6950"},{"last_name":"Hviding","full_name":"Hviding, Raphael E.","first_name":"Raphael E."},{"first_name":"Gabriel","full_name":"Brammer, Gabriel","last_name":"Brammer"},{"last_name":"Simcoe","full_name":"Simcoe, Robert A.","first_name":"Robert A."},{"last_name":"Bose","first_name":"Sownak","full_name":"Bose, Sownak"},{"last_name":"Bouwens","first_name":"Rychard","full_name":"Bouwens, Rychard"},{"full_name":"Dayal, Pratika","first_name":"Pratika","last_name":"Dayal"},{"full_name":"Eilers, Anna Christina","first_name":"Anna Christina","last_name":"Eilers"},{"last_name":"Fei","first_name":"Qinyue","full_name":"Fei, Qinyue"},{"first_name":"Lukas J.","full_name":"Furtak, Lukas J.","last_name":"Furtak"},{"first_name":"Rashmi","full_name":"Gottumukkala, Rashmi","last_name":"Gottumukkala"},{"last_name":"Goulding","full_name":"Goulding, Andy","first_name":"Andy"},{"first_name":"Kasper E.","full_name":"Heintz, Kasper E.","last_name":"Heintz"},{"full_name":"Hirschmann, Michaela","first_name":"Michaela","last_name":"Hirschmann"},{"first_name":"Vasily","full_name":"Kokorev, Vasily","last_name":"Kokorev"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"last_name":"Liu","full_name":"Liu, Zhaoran","first_name":"Zhaoran"},{"full_name":"Natarajan, Priyamvada","first_name":"Priyamvada","last_name":"Natarajan"},{"full_name":"Santarelli, Andrew D.","first_name":"Andrew D.","last_name":"Santarelli"},{"first_name":"David J.","full_name":"Setton, David J.","last_name":"Setton"},{"last_name":"Smith","first_name":"Aaron","full_name":"Smith, Aaron"},{"first_name":"Sandro","full_name":"Tacchella, Sandro","last_name":"Tacchella"},{"first_name":"Marta","full_name":"Volonteri, Marta","last_name":"Volonteri"},{"last_name":"Walter","first_name":"Fabian","full_name":"Walter, Fabian"},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"last_name":"Williams","full_name":"Williams, Christina C.","first_name":"Christina C."}],"doi":"10.33232/001c.162505","_id":"21951","project":[{"_id":"bd9b2118-d553-11ed-ba76-db24564edfea","grant_number":"101076224","name":"Young galaxies as tracers and agents of cosmic reionization"}],"publication":"The Open Journal of Astrophysics","type":"journal_article","citation":{"ama":"Sun WQ, Naidu RP, Matthee JJ, et al. Little Red Dot - Host Galaxy = Black Hole Star: A gas-enshrouded heart at the center of every Little Red Dot. <i>The Open Journal of Astrophysics</i>. 2026;9. doi:<a href=\"https://doi.org/10.33232/001c.162505\">10.33232/001c.162505</a>","apa":"Sun, W. Q., Naidu, R. P., Matthee, J. J., De Graaff, A., Chisholm, J., Greene, J. E., … Williams, C. C. (2026). Little Red Dot - Host Galaxy = Black Hole Star: A gas-enshrouded heart at the center of every Little Red Dot. <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing. <a href=\"https://doi.org/10.33232/001c.162505\">https://doi.org/10.33232/001c.162505</a>","mla":"Sun, Wendy Q., et al. “Little Red Dot - Host Galaxy = Black Hole Star: A Gas-Enshrouded Heart at the Center of Every Little Red Dot.” <i>The Open Journal of Astrophysics</i>, vol. 9, Maynooth Academic Publishing, 2026, doi:<a href=\"https://doi.org/10.33232/001c.162505\">10.33232/001c.162505</a>.","ieee":"W. Q. Sun <i>et al.</i>, “Little Red Dot - Host Galaxy = Black Hole Star: A gas-enshrouded heart at the center of every Little Red Dot,” <i>The Open Journal of Astrophysics</i>, vol. 9. Maynooth Academic Publishing, 2026.","short":"W.Q. Sun, R.P. Naidu, J.J. Matthee, A. De Graaff, J. Chisholm, J.E. Greene, P.A. Oesch, A. Torralba Torregrosa, R.E. Hviding, G. Brammer, R.A. Simcoe, S. Bose, R. Bouwens, P. Dayal, A.C. Eilers, Q. Fei, L.J. Furtak, R. Gottumukkala, A. Goulding, K.E. Heintz, M. Hirschmann, V. Kokorev, J. Leja, Z. Liu, P. Natarajan, A.D. Santarelli, D.J. Setton, A. Smith, S. Tacchella, M. Volonteri, F. Walter, A. Weibel, C.C. Williams, The Open Journal of Astrophysics 9 (2026).","chicago":"Sun, Wendy Q., Rohan P. Naidu, Jorryt J Matthee, Anna De Graaff, John Chisholm, Jenny E. Greene, Pascal A. Oesch, et al. “Little Red Dot - Host Galaxy = Black Hole Star: A Gas-Enshrouded Heart at the Center of Every Little Red Dot.” <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing, 2026. <a href=\"https://doi.org/10.33232/001c.162505\">https://doi.org/10.33232/001c.162505</a>.","ista":"Sun WQ, Naidu RP, Matthee JJ, De Graaff A, Chisholm J, Greene JE, Oesch PA, Torralba Torregrosa A, Hviding RE, Brammer G, Simcoe RA, Bose S, Bouwens R, Dayal P, Eilers AC, Fei Q, Furtak LJ, Gottumukkala R, Goulding A, Heintz KE, Hirschmann M, Kokorev V, Leja J, Liu Z, Natarajan P, Santarelli AD, Setton DJ, Smith A, Tacchella S, Volonteri M, Walter F, Weibel A, Williams CC. 2026. Little Red Dot - Host Galaxy = Black Hole Star: A gas-enshrouded heart at the center of every Little Red Dot. The Open Journal of Astrophysics. 9."},"acknowledgement":"We thank the two anonymous referees for their insightful comments that have strengthened this work.\r\nWQS and RPN acknowledge funding from JWST programs GO-3516, GO-5224, and the MIT Undergraduate\r\nResearch Opportunities Program (UROP). Support for\r\nthis work was provided by NASA through the NASA\r\nHubble Fellowship grant HST-HF2-51515.001-A awarded\r\nby the Space Telescope Science Institute, which is operated by the Association of Universities for Research in\r\nAstronomy, Incorporated, under NASA contract NAS5-\r\n26555. RPN thanks Neil Pappalardo and Jane Pappalardo for their generous support of the MIT Pappalardo Fellowships in Physics, and for their enthusiasm\r\nand encouragement for pursuing the earliest galaxies and\r\nblack holes. JM and AT acknowledge funding from the\r\nEuropean Union (ERC, AGENTS, 101076224). KEH\r\nacknowledges support from the Independent Research Fund Denmark (DFF) under grant 5251-00009B and cofunding by the European Union (ERC, HEAVYMETAL,\r\n101071865). Views and opinions expressed are, however,\r\nthose of the authors only and do not necessarily reflect\r\nthose of the European Union or the European Research\r\nCouncil. Neither the European Union nor the granting\r\nauthority can be held responsible for them. REH acknowledges support by the German Aerospace Center\r\n(DLR) and the Federal Ministry for Economic Affairs\r\nand Energy (BMWi) through program 50OR2403 ‘RUBIES’.\r\nThe data products presented herein were retrieved\r\nfrom the Dawn JWST Archive (DJA). DJA is an initiative of the Cosmic Dawn Center (DAWN), which is\r\nfunded by the Danish National Research Foundation under grant DNRF140. This work is based on observations\r\nmade with the NASA/ESA/CSA James Webb Space\r\nTelescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope\r\nScience Institute, which is operated by the Association\r\nof Universities for Research in Astronomy, Inc., under\r\nNASA contract NAS 5-03127 for JWST. Support for\r\nprograms #3516, #5224, #5664 was provided by NASA\r\nthrough grants from the Space Telescope Science Institute, which is operated by the Association of Universities\r\nfor Research in Astronomy, Inc., under NASA contract\r\nNAS 5-03127.\r\nThe spectra used in this paper are associated with programs 1180 (D’Eugenio et al. 2025d), 1181 (PI: D. Eisenstein), 1208 (Willott et al. 2022), 1210 (PI: N. Luetzgendorf), 1211 (Maseda et al. 2024), 1212 - 1215 (PI: N.\r\nLuetzgendorf), 1228 (Luhman et al. 2024b), 1229 (Luhman et al. 2024a), 1286 (PI: N. Luetzgendorf), 1287 (PI:\r\nK. Isaak), 1345 (Finkelstein et al. 2023), 1433 (Hsiao\r\net al. 2024), 1747 (PI: G. Roberts-Borsani), 2028 (Wang\r\net al. 2024c), 2073 (PI: J. Hennawi), 2198 (Barrufet\r\net al. 2025), 2282 (Bradley et al. 2023), 2561 (Bezanson\r\net al. 2024), 2565 (Nanayakkara et al. 2025), 2640 (PI:\r\nW. Best), 2750 (Arrabal Haro et al. 2023), 2756 (Mascia et al. 2024), 2767 (Williams et al. 2023b), 2770 (PI:\r\nM. McCaughrean), 3073 (Castellano et al. 2024), 3215\r\n(Eisenstein et al. 2025), 4106 (PI: E. Nelson), 4233 (de\r\nGraaff et al. 2025c), 4446 (Frye et al. 2024), 4557 (PI: H.\r\nYan), 5105 (Shen et al. 2024), 5224 (PIs: P.A. Oesch &\r\nR.P. Naidu), 6368 (PI: M. Dickinson), 6541 (DeCoursey\r\net al. 2025), 6585 (PI: D. Coulter), 6642 (PI: J. Muzerolle\r\nPage), and FRESCO IFU (Matthee et al. 2024; Torralba\r\net al. 2025b).\r\nSoftware used in developing this work includes:\r\nmatplotlib (Hunter 2007), jupyter (Kluyver et al.\r\n2016), IPython (P´erez & Granger 2007), numpy\r\n(Oliphant 2015), scipy (Virtanen et al. 2020), TOPCAT\r\n(Taylor 2005), Astropy (Astropy Collaboration et al.\r\n2013), msaexp (Brammer 2023).","ddc":["520"],"external_id":{"arxiv":["2601.20929"]},"arxiv":1,"intvolume":"         9","title":"Little Red Dot - Host Galaxy = Black Hole Star: A gas-enshrouded heart at the center of every Little Red Dot","DOAJ_listed":"1","language":[{"iso":"eng"}],"file_date_updated":"2026-06-08T08:23:37Z","volume":9,"day":"25","abstract":[{"lang":"eng","text":"The central engines of Little Red Dots (LRDs) may be “black hole stars” (BH*s), early stages of\r\nblack hole growth characterized by dense gas envelopes. So far, the most direct evidence for BH*s\r\ncomes from a handful of sources where the host galaxy is completely outshone as suggested by their\r\nremarkably steep Balmer breaks. Here we present a novel scheme to disentangle BH*s from their\r\nhost galaxies assuming that the [O III]5008˚A line arises exclusively from the host. Using a sample\r\nof 98 LRDs (z ≈ 2 − 9) with high quality NIRSpec/PRISM spectra, we demonstrate that the hostsubtracted median stack displays a Balmer break > 2× stronger than massive quiescent galaxies,\r\nwith the rest-optical continuum resembling a blackbody-like SED (Teff ≈ 4050 K, log(Lbol) ≈ 43.9\r\nerg s−1\r\n, Reff ≈ 1300 au). We measure a steep Balmer decrement (Hα/Hβ > 10) and numerous\r\ndensity-sensitive features (e.g., Fe II, He I, O I). These are hallmark signatures of dense gas envelopes,\r\nproviding population-level evidence that BH*s indeed power LRDs. In the median LRD, BH*s account\r\nfor ∼ 20% of the UV emission, ∼ 50% at the Balmer break, and ∼ 90% at wavelengths longer\r\nthan Hα with the remainder arising from the host. BH*s preferentially reside in low-mass galaxies\r\n(M⋆ ≈ 108 M⊙) undergoing recent starbursts, as evidenced by extreme emission line EWs (e.g.,\r\n[O III]5008˚A≈ 1100˚A, C III]≈ 12˚A), thereby favoring BH* origins linked to star-formation. We show\r\nV-shaped LRD selections are biased to high BH*/host fractions (≳ 60% at 5500˚A) – less dominant\r\nBH*s may be powering JWST’s blue broad-line AGN. We find BH*s are so commonplace and transient\r\n(duty cycle ∼ 1%, lifetime ∼ 10 Myrs) that every massive black hole may have once shone as a BH*.\r\n"}],"date_created":"2026-06-07T22:01:36Z","scopus_import":"1","status":"public","year":"2026","has_accepted_license":"1","OA_place":"publisher","publication_identifier":{"eissn":["2565-6120"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"success":1,"creator":"dernst","checksum":"33c4a444f7c37b3f47ecbd53eb187c1b","content_type":"application/pdf","file_size":7591188,"access_level":"open_access","date_updated":"2026-06-08T08:23:37Z","relation":"main_file","file_name":"2026_OpenJourAstrophysics_Sun.pdf","date_created":"2026-06-08T08:23:37Z","file_id":"21952"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"diamond","oa":1,"article_processing_charge":"No","department":[{"_id":"JoMa"}],"month":"05","date_published":"2026-05-25T00:00:00Z","article_type":"original","date_updated":"2026-06-08T08:25:40Z","publication_status":"published","PlanS_conform":"1","publisher":"Maynooth Academic Publishing"},{"file_date_updated":"2026-06-10T07:58:58Z","volume":68,"title":"Train-free segmentation in MRI with cubical persistent homology","language":[{"iso":"eng"}],"day":"25","abstract":[{"text":"We investigate a framework for train-free MRI segmentation based on Topological Data Analysis. The pipeline proceeds in three steps, first identifying the whole object to segment via automatic thresholding, then detecting a distinctive subset whose topology is known in advance, and finally deducing the various components of the segmentation. A key ingredient is the extraction of approximate representative cycles from persistence diagrams, which provides an interpretable link between persistent features and anatomical components. To clarify the method’s scope, we make the underlying topological and intensity assumptions explicit, quantify when they hold on real data, and analyze typical failure modes. We evaluate the approach on glioblastoma and on fetal cortical plate segmentation, with comparisons to unsupervised and deep-learning references. By operating without large annotated datasets, the method is well suited to scarce-data settings and provides an interpretable baseline and practical initialization for expert refinement or learning-based pipelines.","lang":"eng"}],"date_created":"2026-06-08T08:34:43Z","scopus_import":"1","author":[{"last_name":"François","full_name":"François, Anton","first_name":"Anton"},{"last_name":"Tinarrage","orcid":"0000-0002-1404-1095","id":"40ebcc9d-905f-11ef-bf0a-dc475da8a04e","full_name":"Tinarrage, Raphaël","first_name":"Raphaël"}],"quality_controlled":"1","doi":"10.1007/s10851-026-01300-1","_id":"21954","publication":"Journal of Mathematical Imaging and Vision","type":"journal_article","arxiv":1,"intvolume":"        68","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","citation":{"ista":"François A, Tinarrage R. 2026. Train-free segmentation in MRI with cubical persistent homology. Journal of Mathematical Imaging and Vision. 68(3), 20.","short":"A. François, R. Tinarrage, Journal of Mathematical Imaging and Vision 68 (2026).","chicago":"François, Anton, and Raphaël Tinarrage. “Train-Free Segmentation in MRI with Cubical Persistent Homology.” <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s10851-026-01300-1\">https://doi.org/10.1007/s10851-026-01300-1</a>.","ieee":"A. François and R. Tinarrage, “Train-free segmentation in MRI with cubical persistent homology,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 68, no. 3. Springer Nature, 2026.","mla":"François, Anton, and Raphaël Tinarrage. “Train-Free Segmentation in MRI with Cubical Persistent Homology.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 68, no. 3, 20, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s10851-026-01300-1\">10.1007/s10851-026-01300-1</a>.","ama":"François A, Tinarrage R. Train-free segmentation in MRI with cubical persistent homology. <i>Journal of Mathematical Imaging and Vision</i>. 2026;68(3). doi:<a href=\"https://doi.org/10.1007/s10851-026-01300-1\">10.1007/s10851-026-01300-1</a>","apa":"François, A., &#38; Tinarrage, R. (2026). Train-free segmentation in MRI with cubical persistent homology. <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10851-026-01300-1\">https://doi.org/10.1007/s10851-026-01300-1</a>"},"external_id":{"arxiv":["2401.01160"]},"ddc":["510"],"oa":1,"department":[{"_id":"UlWa"}],"article_number":"20","article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","date_published":"2026-05-25T00:00:00Z","month":"05","article_type":"original","date_updated":"2026-06-10T08:00:52Z","publication_status":"published","publisher":"Springer Nature","status":"public","issue":"3","year":"2026","has_accepted_license":"1","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"issn":["0924-9907"],"eissn":["1573-7683"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"hybrid","file":[{"date_updated":"2026-06-10T07:58:58Z","success":1,"content_type":"application/pdf","checksum":"34080653e0f9c6160856a6bbca9b5248","file_size":6070434,"access_level":"open_access","creator":"dernst","file_id":"21990","relation":"main_file","date_created":"2026-06-10T07:58:58Z","file_name":"2026_JourMathImaging_Francois.pdf"}],"oa_version":"Published Version"},{"year":"2026","status":"public","OA_type":"green","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","publication_identifier":{"issn":["0896-6273"],"eissn":[" 1097-4199"]},"department":[{"_id":"AmDo"}],"article_processing_charge":"No","oa":1,"publisher":"Elsevier","date_published":"2026-06-03T00:00:00Z","article_type":"original","month":"06","publication_status":"inpress","date_updated":"2026-06-16T08:35:11Z","doi":"10.1016/j.neuron.2026.05.010","_id":"21955","author":[{"full_name":"Walker, Samuel J.","first_name":"Samuel J.","last_name":"Walker"},{"first_name":"Elijah D.","full_name":"Lowenstein, Elijah D.","last_name":"Lowenstein"},{"orcid":"0000-0001-5398-6473","last_name":"Douglass","first_name":"Amelia May Barnett","full_name":"Douglass, Amelia May Barnett","id":"de5f6fda-80fb-11ef-996f-a8c4ecd8e289"},{"last_name":"Thomas","first_name":"Callum M.P.","full_name":"Thomas, Callum M.P."},{"last_name":"Madara","full_name":"Madara, Joseph C.","first_name":"Joseph C."},{"full_name":"Kucukdereli, Hakan","first_name":"Hakan","last_name":"Kucukdereli"},{"first_name":"Eunice A.","full_name":"Barbosa-Meillon, Eunice A.","last_name":"Barbosa-Meillon"},{"full_name":"Tao, Jenkang","first_name":"Jenkang","last_name":"Tao"},{"full_name":"Resch, Jon M.","first_name":"Jon M.","last_name":"Resch"},{"first_name":"Bradford B.","full_name":"Lowell, Bradford B.","last_name":"Lowell"}],"quality_controlled":"1","acknowledgement":"We thank all members of the B.B.L. laboratory for helpful discussions. We\r\nthank the BADERC and BNORC transgenic cores (NIH P30DK057521 and\r\nP30DK046200) for performing embryo injections to generate knockin mouse\r\nlines. We also thank the BIDMC Energy Balance Core (supported by NIH\r\nS10OD028635 and the Boston Area Diabetes Endocrinology Research Centers, P30DK135043), where Marissa Cortopassi performed indirect calorimetry experiments and Alexander Banks assisted with data analysis and interpretation. Confocal imaging was performed at BIDMC’s Confocal Imaging\r\nCore. We thank Chen Wu for assistance in designing knockin mouse lines.\r\nThis work was supported by the NIH (R01DK134427, R01DK096010, and\r\nR01DK075632 to B.B.L.). Authors were supported by an EMBO Long-Term\r\nFellowship (770-2018, S.J.W.), a T32 Postdoctoral Training Fellowship\r\n(5T32DK007516, E.D.L.), the Charles A. King Trust Postdoctoral Research\r\nFellowship program (A.M.D.), and a K99 Career Development Award\r\n(K99HL144923, J.M.R.).","citation":{"ista":"Walker SJ, Lowenstein ED, Douglass AM, Thomas CMP, Madara JC, Kucukdereli H, Barbosa-Meillon EA, Tao J, Resch JM, Lowell BB. A hypothalamic circuit for anticipating future changes in energy balance. Neuron.","short":"S.J. Walker, E.D. Lowenstein, A.M. Douglass, C.M.P. Thomas, J.C. Madara, H. Kucukdereli, E.A. Barbosa-Meillon, J. Tao, J.M. Resch, B.B. Lowell, Neuron (n.d.).","chicago":"Walker, Samuel J., Elijah D. Lowenstein, Amelia M. Douglass, Callum M.P. Thomas, Joseph C. Madara, Hakan Kucukdereli, Eunice A. Barbosa-Meillon, Jenkang Tao, Jon M. Resch, and Bradford B. Lowell. “A Hypothalamic Circuit for Anticipating Future Changes in Energy Balance.” <i>Neuron</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.neuron.2026.05.010\">https://doi.org/10.1016/j.neuron.2026.05.010</a>.","mla":"Walker, Samuel J., et al. “A Hypothalamic Circuit for Anticipating Future Changes in Energy Balance.” <i>Neuron</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.neuron.2026.05.010\">10.1016/j.neuron.2026.05.010</a>.","ieee":"S. J. Walker <i>et al.</i>, “A hypothalamic circuit for anticipating future changes in energy balance,” <i>Neuron</i>. Elsevier.","ama":"Walker SJ, Lowenstein ED, Douglass AM, et al. A hypothalamic circuit for anticipating future changes in energy balance. <i>Neuron</i>. doi:<a href=\"https://doi.org/10.1016/j.neuron.2026.05.010\">10.1016/j.neuron.2026.05.010</a>","apa":"Walker, S. J., Lowenstein, E. D., Douglass, A. M., Thomas, C. M. P., Madara, J. C., Kucukdereli, H., … Lowell, B. B. (n.d.). A hypothalamic circuit for anticipating future changes in energy balance. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2026.05.010\">https://doi.org/10.1016/j.neuron.2026.05.010</a>"},"external_id":{"pmid":["42235510"]},"publication":"Neuron","type":"journal_article","day":"03","abstract":[{"text":"AgRP neurons cause hunger, the drive to seek and consume food. Their activation by fasting is key for survival and is thought to be triggered by feedback when energy stores are low. However, we know that environmental cues can also regulate AgRP neurons since cues that predict future food intake rapidly inhibit AgRP neurons, but is the converse true: can the prediction of future fasting rapidly activate AgRP neurons? Here, we show in mice that such rapid fasting activation of AgRP neurons does occur. This rapid activation is driven by excitatory input from paraventricular hypothalamic (PVH) neurons expressing Sim2, which are bidirectionally sensitive to predictions of future energy state. Thus, cognitively processed contextual information conveyed by PVHSim2 neurons strongly activates AgRP neurons. Lastly, chronic silencing of PVHSim2 neurons causes persistent hypophagia. This PVHSim2-to-AgRP-neuron circuit, by anticipating and preventing negative energy balance, provides an important new dimension of hunger regulation.","lang":"eng"}],"date_created":"2026-06-08T09:24:25Z","keyword":["hunger","hypothalamus","AGRP neurons","neuroscience","metabolism","homeostasis","feeding","food intake","energy balance","appetite"],"title":"A hypothalamic circuit for anticipating future changes in energy balance","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.09.27.678865"}],"language":[{"iso":"eng"}],"pmid":1,"scopus_import":"1"},{"supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"date_created":"2026-06-08T13:29:52Z","day":"09","abstract":[{"text":"This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.\r\n\r\nIn the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks.","lang":"eng"}],"file_date_updated":"2026-06-10T13:33:25Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"21144","status":"public"}]},"language":[{"iso":"eng"}],"title":"Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames","ddc":["500"],"citation":{"mla":"Zapata, Jeferson. <i>Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21957\">10.15479/AT-ISTA-21957</a>.","ieee":"J. Zapata, “Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames,” Institute of Science and Technology Austria, 2026.","apa":"Zapata, J. (2026). <i>Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21957\">https://doi.org/10.15479/AT-ISTA-21957</a>","ama":"Zapata J. Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21957\">10.15479/AT-ISTA-21957</a>","ista":"Zapata J. 2026. Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.","chicago":"Zapata, Jeferson. “Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21957\">https://doi.org/10.15479/AT-ISTA-21957</a>.","short":"J. Zapata, Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026."},"acknowledgement":"Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.","type":"dissertation","project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35"}],"_id":"21957","doi":"10.15479/AT-ISTA-21957","page":"89","author":[{"last_name":"Zapata","first_name":"Jeferson","full_name":"Zapata, Jeferson","id":"00223538-AF8F-11E9-A4C7-F729E6697425"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","date_updated":"2026-06-12T10:37:00Z","date_published":"2026-06-09T00:00:00Z","month":"06","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"article_processing_charge":"No","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"file":[{"file_name":"istaustriathesis_JZapata.zip","date_created":"2026-06-08T13:20:02Z","relation":"source_file","file_id":"21958","creator":"jzapata","file_size":40811933,"access_level":"closed","checksum":"b11a959e99d3dcf61040282b5c837141","content_type":"application/zip","date_updated":"2026-06-08T13:20:02Z"},{"file_id":"21992","relation":"main_file","file_name":"4_Final_Thesis_JZapata_REX.pdf","date_created":"2026-06-10T13:33:25Z","date_updated":"2026-06-10T13:33:25Z","success":1,"creator":"jzapata","content_type":"application/pdf","access_level":"open_access","file_size":2207892,"checksum":"edf1e5899b2e31505cd1aa3fe8bd4b7f"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-079-4"]},"OA_place":"publisher","corr_author":"1","has_accepted_license":"1","year":"2026","status":"public","degree_awarded":"PhD"},{"date_published":"2026-06-16T00:00:00Z","month":"06","date_updated":"2026-06-16T08:00:38Z","contributor":[{"last_name":"Kerschbaumer","contributor_type":"contact_person","orcid":"0009-0002-2370-8661","id":"ade85a9c-3200-11ee-973b-91c1eb240410","first_name":"Aron"},{"last_name":"Serbyn","contributor_type":"supervisor","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","first_name":"Jean-Yves Marc","contributor_type":"researcher","last_name":"Desaules","orcid":"0000-0002-3749-6375"},{"first_name":"Marko","last_name":"Ljubotina","contributor_type":"researcher"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2026-06-15T22:02:07Z","title":"Research Data: \"Quasi-solitons in Rydberg atom chains\"","oa":1,"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"day":"16","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Solitons - localized wave packets that travel without spreading - play a central role in understanding transport and properties of nonlinear systems. In quantum many-body systems, however, such robust excitations are typically destroyed by thermalization. Here, we theoretically demonstrate the existence of solitonic excitations in high-energy states of Rydberg atom chains in the regime of strong nearest-neighbor Rydberg blockade. \r\nThese localized wave packets propagate directionally atop a special class of reviving initial states related to quantum many-body scars and are capable of carrying energy. Exhibiting long coherence times, these states constitute a form of non-ergodic quantum dynamics and can be efficiently implemented on Rydberg atom simulators. In this work, in addition to a phenomenological description of solitons, we identify their counterpart in a classical nonlinear dynamical system, demonstrate their potential use in quantum information transfer, and conjecture their relevance for anomalous energy transport reported in numerical studies of Rydberg atom arrays."}],"date_created":"2026-06-09T07:17:50Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","type":"research_data","OA_place":"repository","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"file_name":"README.txt","date_created":"2026-06-15T22:01:57Z","relation":"main_file","file_id":"22010","creator":"akerschb","content_type":"text/plain","access_level":"open_access","checksum":"133269a105e996c6c44fdd56128259c7","file_size":1940,"success":1,"date_updated":"2026-06-15T22:01:57Z"},{"date_updated":"2026-06-15T22:02:07Z","success":1,"access_level":"open_access","checksum":"759f9649c3919f4c4ad37a1d104ea32a","content_type":"application/zip","file_size":13259747,"creator":"akerschb","file_id":"22011","relation":"main_file","date_created":"2026-06-15T22:02:07Z","file_name":"Soliton_Data.zip"}],"citation":{"apa":"Kerschbaumer, A. (2026). Research Data: “Quasi-solitons in Rydberg atom chains.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21960\">https://doi.org/10.15479/AT-ISTA-21960</a>","ama":"Kerschbaumer A. Research Data: “Quasi-solitons in Rydberg atom chains.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21960\">10.15479/AT-ISTA-21960</a>","ieee":"A. Kerschbaumer, “Research Data: ‘Quasi-solitons in Rydberg atom chains.’” Institute of Science and Technology Austria, 2026.","mla":"Kerschbaumer, Aron. <i>Research Data: “Quasi-Solitons in Rydberg Atom Chains.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21960\">10.15479/AT-ISTA-21960</a>.","chicago":"Kerschbaumer, Aron. “Research Data: ‘Quasi-Solitons in Rydberg Atom Chains.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21960\">https://doi.org/10.15479/AT-ISTA-21960</a>.","short":"A. Kerschbaumer, (2026).","ista":"Kerschbaumer A. 2026. Research Data: ‘Quasi-solitons in Rydberg atom chains’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21960\">10.15479/AT-ISTA-21960</a>."},"oa_version":"Published Version","year":"2026","author":[{"id":"ade85a9c-3200-11ee-973b-91c1eb240410","first_name":"Aron","full_name":"Kerschbaumer, Aron","last_name":"Kerschbaumer","orcid":"0009-0002-2370-8661"}],"status":"public","has_accepted_license":"1","corr_author":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"doi":"10.15479/AT-ISTA-21960","_id":"21960"},{"title":"Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner","main_file_link":[{"url":"https://doi.org/10.64898/2026.05.01.722172","open_access":"1"}],"language":[{"iso":"eng"}],"day":"05","abstract":[{"text":"The generation of faithful cell-type diversity and correct projection neuron numbers is essential for cerebral cortex development. Corticogenesis is however susceptible to genetic interference of critical signaling pathways, including mutations in Mtor/Rptor that lead to microcephaly. How the loss of Rptor/mTORC1 function affects cortical developmental programs, at single cell level, is still unknown. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to probe Rptor gene function upon sparse single cell- or global tissue-wide ablation. We found that tissue-wide effects drive the etiology of cortical microcephaly upon loss of Rptor, rather than deficits in projection neuron genesis. Conversely, Rptor function is cell-autonomously required for postnatal projection neuron survival in a highly cell-type-specific manner. Collectively, our results suggest that the fine balance of precise cell-type-specific cell-autonomous Rptor/mTORC1 function in concert with non-cell-autonomous tissue-wide effects is essential for the development of a properly-sized cerebral cortex with accurate projection neuron diversity.","lang":"eng"}],"date_created":"2026-06-09T08:08:18Z","type":"preprint","publication":"bioRxiv","citation":{"ieee":"A. Villalba Requena <i>et al.</i>, “Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner,” <i>bioRxiv</i>. .","mla":"Villalba Requena, Ana, et al. “Mtor/Rptor Function Globally Prevents Cortical Microcephaly and Cell-Autonomously Promotes Postnatal Neuron Survival in Cell Type Specific Manner.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.64898/2026.05.01.722172\">10.64898/2026.05.01.722172</a>.","apa":"Villalba Requena, A., Beattie, R. J., Pauler, F., Streicher, C., Miranda, O., Krausgruber, T., … Hippenmeyer, S. (n.d.). Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2026.05.01.722172\">https://doi.org/10.64898/2026.05.01.722172</a>","ama":"Villalba Requena A, Beattie RJ, Pauler F, et al. Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.64898/2026.05.01.722172\">10.64898/2026.05.01.722172</a>","ista":"Villalba Requena A, Beattie RJ, Pauler F, Streicher C, Miranda O, Krausgruber T, Senekowitsch M, Farlik M, Bock C, Rülicke T, Hippenmeyer S. Mtor/Rptor function globally prevents cortical microcephaly and cell-autonomously promotes postnatal neuron survival in cell type specific manner. bioRxiv, <a href=\"https://doi.org/10.64898/2026.05.01.722172\">10.64898/2026.05.01.722172</a>.","chicago":"Villalba Requena, Ana, Robert J Beattie, Florian Pauler, Carmen Streicher, Osvaldo Miranda, Thomas Krausgruber, Martin Senekowitsch, et al. “Mtor/Rptor Function Globally Prevents Cortical Microcephaly and Cell-Autonomously Promotes Postnatal Neuron Survival in Cell Type Specific Manner.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.64898/2026.05.01.722172\">https://doi.org/10.64898/2026.05.01.722172</a>.","short":"A. Villalba Requena, R.J. Beattie, F. Pauler, C. Streicher, O. Miranda, T. Krausgruber, M. Senekowitsch, M. Farlik, C. Bock, T. Rülicke, S. Hippenmeyer, BioRxiv (n.d.)."},"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer (VBCF GmbH, NGS Unit), and A.\r\nNicolas (IST Austria Lab Support Facility / Mass Spectrometry Facility) for technical support; K. Ferencak,\r\nI. Aykara, P. Hirschfeld, E. Fisher, S. Laukoter, L. Andersen for initial experiments and/or assistance; and\r\nall members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service\r\nUnits (SSU) of IST Austria through resources provided by the Imaging and Optics- (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF). R.B. received support from FWF Meitner-Programm (M 2416). This\r\nwork was also supported by IST Austria institutional funds; the People Programme (Marie Curie Actions)\r\nof the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement\r\nNo 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020\r\nresearch and innovation programme (grant agreement No 725780 LinPro) to S.H.","ddc":["570"],"author":[{"orcid":"0000-0002-5615-5277","last_name":"Villalba Requena","full_name":"Villalba Requena, Ana","first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"last_name":"Miranda","orcid":"0000-0001-6618-6889","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo","first_name":"Osvaldo"},{"full_name":"Krausgruber, Thomas","first_name":"Thomas","last_name":"Krausgruber"},{"last_name":"Senekowitsch","first_name":"Martin","full_name":"Senekowitsch, Martin"},{"first_name":"Matthias","full_name":"Farlik, Matthias","last_name":"Farlik"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"}],"doi":"10.64898/2026.05.01.722172","_id":"21962","date_published":"2026-05-05T00:00:00Z","month":"05","date_updated":"2026-06-16T08:45:25Z","publication_status":"submitted","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"MassSpec"},{"_id":"Bio"}],"oa":1,"department":[{"_id":"SiHi"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"OA_type":"green","oa_version":"Preprint","year":"2026","status":"public","has_accepted_license":"1"},{"ddc":["570"],"acknowledgement":"We thank Kay-Uwe Wagner (Wayne State University) for generously sharing Jak1/2–flox mouse lines; A.\r\nSommer (VBCF GmbH, NGS Unit) for technical support; N. Kim, V. Mick, S. Schnabl, S. Gobeil, and L.\r\nAndersen for technical assistance; all members of the Hippenmeyer lab for discussion and B. Novitch for\r\ncomments on earlier versions of the manuscript. This research was supported by the Scientific Service Units\r\n(SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF). O.A.M received support from the Austrian Academy of Sciences\r\nÖAW (DOC 186584), and N.A. from FWF Elise Richter Program (Grant V1041T). This work was also\r\nsupported by IST Austria institutional funds; FWF SFB F78 (Neuro Stem Modulation) to S.H., and the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (grant agreement No 725780 LinPro) to S.H.","citation":{"ista":"Miranda O, Contreras X, Pauler F, Davaatseren A, Amberg N, Streicher C, Villalba Requena A, Heger A-M, Marie C, Hassan BA, Rülicke T, Hippenmeyer S. Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. bioRxiv, <a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>.","chicago":"Miranda, Osvaldo, Ximena Contreras, Florian Pauler, Amarbayasgalan Davaatseren, Nicole Amberg, Carmen Streicher, Ana Villalba Requena, et al. “Pten Orchestrates Neurogenic Radial Glia Lineage Progression and Tunes Neocortical Astrocyte Production.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.64898/2026.05.01.722191\">https://doi.org/10.64898/2026.05.01.722191</a>.","short":"O. Miranda, X. Contreras, F. Pauler, A. Davaatseren, N. Amberg, C. Streicher, A. Villalba Requena, A.-M. Heger, C. Marie, B.A. Hassan, T. Rülicke, S. Hippenmeyer, BioRxiv (n.d.).","ieee":"O. Miranda <i>et al.</i>, “Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production,” <i>bioRxiv</i>. .","mla":"Miranda, Osvaldo, et al. “Pten Orchestrates Neurogenic Radial Glia Lineage Progression and Tunes Neocortical Astrocyte Production.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>.","apa":"Miranda, O., Contreras, X., Pauler, F., Davaatseren, A., Amberg, N., Streicher, C., … Hippenmeyer, S. (n.d.). Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2026.05.01.722191\">https://doi.org/10.64898/2026.05.01.722191</a>","ama":"Miranda O, Contreras X, Pauler F, et al. Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>"},"type":"preprint","publication":"bioRxiv","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"_id":"21963","doi":"10.64898/2026.05.01.722191","author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo","full_name":"Miranda, Osvaldo","last_name":"Miranda","orcid":"0000-0001-6618-6889"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"id":"70ADC922-B424-11E9-99E3-BA18E6697425","first_name":"Amarbayasgalan","full_name":"Davaatseren, Amarbayasgalan","last_name":"Davaatseren"},{"first_name":"Nicole","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Villalba Requena, Ana","first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","last_name":"Villalba Requena"},{"last_name":"Heger","first_name":"Anna-Magdalena","full_name":"Heger, Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marie, Corentine","first_name":"Corentine","last_name":"Marie"},{"last_name":"Hassan","full_name":"Hassan, Bassem A.","first_name":"Bassem A."},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2026-06-09T08:08:53Z","abstract":[{"lang":"eng","text":"The cerebral cortex consists of immense numbers of neuronal and glial cell-types derived from radial glial progenitor (RGP) cells. How RGPs generate appropriate quantities of distinct cortical cell-types to safeguard a brain of correct size, is not well understood. However, genetic aberration in human, including mutations in PTEN, lead to cortical malformation such as macrocephaly, albeit with unknown etiology. Here we utilized Mosaic Analysis with Double Markers (MADM)-based clonal analysis and single cell phenotyping to decipher the role of Pten in neurogenic and gliogenic RGP lineage progression during cortical ontogeny. While neurogenic RGP lineage progression and projection neuron production was moderately altered in the absence of Pten, cortical astrocyte production was drastically increased. Through genetic epistasis experiments we show that the loss of Pten uncouples astrocyte generation from essential growth factor signaling hubs, funneling into MAPK. Collectively, our results suggest that Pten regulates RGP lineage progression with distinct sequential functions in cortical projection neurogenesis and astrocyte production to ensure the emergence of a correctly-sized cerebral cortex."}],"day":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.64898/2026.05.01.722191"}],"language":[{"iso":"eng"}],"title":"Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production","OA_type":"green","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","has_accepted_license":"1","corr_author":"1","year":"2026","status":"public","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"publication_status":"submitted","date_updated":"2026-06-16T08:57:20Z","month":"05","date_published":"2026-05-05T00:00:00Z","department":[{"_id":"SiHi"},{"_id":"PreCl"},{"_id":"GradSch"}],"article_processing_charge":"No","oa":1},{"OA_place":"repository","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","publication":"bioRxiv","citation":{"mla":"Khudiakova, Kseniia, et al. “Sign Epistasis Extends the Effects of Balancing Selection on Genetic Diversity.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>.","ieee":"K. Khudiakova, N. H. Barton, and G. Arnqvist, “Sign epistasis extends the effects of balancing selection on genetic diversity,” <i>bioRxiv</i>. .","ama":"Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of balancing selection on genetic diversity. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>","apa":"Khudiakova, K., Barton, N. H., &#38; Arnqvist, G. (n.d.). Sign epistasis extends the effects of balancing selection on genetic diversity. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.04.09.647826\">https://doi.org/10.1101/2025.04.09.647826</a>","ista":"Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of balancing selection on genetic diversity. bioRxiv, <a href=\"https://doi.org/10.1101/2025.04.09.647826\">10.1101/2025.04.09.647826</a>.","short":"K. Khudiakova, N.H. Barton, G. Arnqvist, BioRxiv (n.d.).","chicago":"Khudiakova, Kseniia, Nicholas H Barton, and Goran Arnqvist. “Sign Epistasis Extends the Effects of Balancing Selection on Genetic Diversity.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.04.09.647826\">https://doi.org/10.1101/2025.04.09.647826</a>."},"acknowledgement":"This work was funded by grants from the Swedish Research Council (2023-03730 to G.A.) and the DOC fellowship from the Austrian Academy of Science (26293 to K.K.).","oa_version":"Preprint","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"OA_type":"green","status":"public","year":"2026","author":[{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","orcid":"0000-0002-6246-1465"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arnqvist","full_name":"Arnqvist, Goran","first_name":"Goran"}],"doi":"10.1101/2025.04.09.647826","_id":"21968","corr_author":"1","project":[{"_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293","name":"The impact of deleterious mutations on small populations"}],"month":"04","date_published":"2026-04-23T00:00:00Z","publication_status":"draft","date_updated":"2026-06-12T12:43:34Z","title":"Sign epistasis extends the effects of balancing selection on genetic diversity","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"21918"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.04.09.647826"}],"language":[{"iso":"eng"}],"oa":1,"day":"23","article_processing_charge":"No","abstract":[{"text":"Balancing selection, a form of selection that maintains genetic diversity, is difficult to detect, and the importance of balancing selection for the maintenance of genetic variation may be larger than often assumed. We model the possibility that the diversity-promoting effects of balancing selection extend to other loci that show sign epistasis with a locus under balancing selection. Rather than focusing on overdominance, as was done in previous efforts, we explore the effects of negative frequency dependence and show that this has important effects on the conditions under which the diversity-promoting effect of epistasis can occur in diploids. Our results show that not only recombination rate but also the dominance of sign epistasis are key parameters that determine the maintenance of polymorphism beyond the locus under direct balancing selection. We suggest that the effect we explore may play a significant role, especially when balancing selection acts on major effect loci.","lang":"eng"}],"date_created":"2026-06-09T12:26:11Z","department":[{"_id":"NiBa"},{"_id":"JaMa"}]},{"tmp":{"legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT","name":"The MIT License"},"file":[{"relation":"main_file","file_name":"LICENSE","date_created":"2026-06-09T19:16:02Z","file_id":"21974","success":1,"creator":"ybleile","content_type":"application/octet-stream","file_size":1081,"access_level":"open_access","checksum":"48f633b6767c4b15dd6220ca2b4dc175","date_updated":"2026-06-09T19:16:02Z"},{"success":1,"creator":"ybleile","file_size":11308032,"access_level":"open_access","content_type":"application/octet-stream","checksum":"de25d0b224acbde3d38f837fdd8f97d5","date_updated":"2026-06-09T19:16:27Z","relation":"main_file","file_name":"quadrix-x64.exe","date_created":"2026-06-09T19:16:27Z","file_id":"21975"},{"date_created":"2026-06-09T19:16:28Z","file_name":"quadrix-arm64.exe","relation":"main_file","file_id":"21976","content_type":"application/octet-stream","checksum":"a7b94a7380dc178e76ebdba9f1fa45c2","access_level":"open_access","file_size":10655744,"creator":"ybleile","success":1,"date_updated":"2026-06-09T19:16:28Z"},{"date_created":"2026-06-09T19:16:27Z","file_name":"Quadrix Desktop.app.zip","relation":"main_file","file_id":"21977","content_type":"application/zip","access_level":"open_access","checksum":"2404aa8619a56668bd95032791ee1250","file_size":2032,"creator":"ybleile","success":1,"date_updated":"2026-06-09T19:16:27Z"},{"creator":"ybleile","content_type":"application/octet-stream","file_size":12187896,"checksum":"106930f81563c5c719a5f4030b5ca5ed","access_level":"open_access","success":1,"date_updated":"2026-06-09T19:16:40Z","file_name":"quadrix-arm64","date_created":"2026-06-09T19:16:40Z","relation":"main_file","file_id":"21978"},{"success":1,"creator":"ybleile","content_type":"application/octet-stream","file_size":20587592,"access_level":"open_access","checksum":"0e6ba129318446676f220087e7e6ff41","date_updated":"2026-06-09T19:16:52Z","relation":"main_file","file_name":"quadrix-x64","date_created":"2026-06-09T19:16:52Z","file_id":"21979"},{"content_type":"application/gzip","checksum":"f0b03385d17df049219465ab7403fe09","file_size":1914198,"access_level":"open_access","creator":"pub-gitlab-bot","date_updated":"2026-06-09T19:19:12Z","date_created":"2026-06-09T19:19:12Z","file_name":"Quadrix.zip","relation":"main_file","file_id":"21972"},{"checksum":"ede0bbb24bf41ab4009cf1b6a9009671","content_type":"application/zip","access_level":"open_access","file_size":37557,"creator":"ybleile","date_updated":"2026-06-10T19:09:38Z","relation":"supplementary_material","date_created":"2026-06-10T19:09:38Z","file_name":"THIRD_PARTY_LICENSES.zip","file_id":"21993"},{"relation":"main_file","date_created":"2026-06-15T08:13:32Z","file_name":"README.md","file_id":"22009","success":1,"access_level":"open_access","content_type":"text/markdown","file_size":3839,"checksum":"f3c5fcc62c88e449ab5c660244df5aef","creator":"ybleile","date_updated":"2026-06-15T08:13:32Z"},{"date_updated":"2026-06-15T08:14:24Z","content_type":"application/gzip","access_level":"open_access","checksum":"aa74828c3165aafcdee4ddcc9ecd37ac","file_size":1912923,"creator":"pub-gitlab-bot","file_id":"22008","date_created":"2026-06-15T08:14:24Z","file_name":"Quadrix.zip","relation":"main_file"}],"citation":{"ista":"Bokor Bleile Y, Cortinovis E. 2026. Quadrix, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>.","chicago":"Bokor Bleile, Yossi, and Emanuele Cortinovis. “Quadrix.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">https://doi.org/10.15479/AT-ISTA-21971</a>.","short":"Y. Bokor Bleile, E. Cortinovis, (2026).","ieee":"Y. Bokor Bleile and E. Cortinovis, “Quadrix.” Institute of Science and Technology Austria, 2026.","mla":"Bokor Bleile, Yossi, and Emanuele Cortinovis. <i>Quadrix</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>.","apa":"Bokor Bleile, Y., &#38; Cortinovis, E. (2026). Quadrix. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21971\">https://doi.org/10.15479/AT-ISTA-21971</a>","ama":"Bokor Bleile Y, Cortinovis E. Quadrix. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21971\">10.15479/AT-ISTA-21971</a>"},"type":"software","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","corr_author":"1","has_accepted_license":"1","project":[{"_id":"9106a876-16d5-11f0-9cad-bbf11c9952f9","grant_number":"ESP 9584724","name":"Quantitative Unbiased Shape Analysis with Geometry & Topology"}],"doi":"10.15479/AT-ISTA-21971","_id":"21971","status":"public","year":"2026","author":[{"first_name":"Yossi","full_name":"Bleile, Yossi","id":"920a7385-7995-11ef-9bfd-8c434cd8f3c2","orcid":"0000-0002-4861-9174","last_name":"Bleile"},{"last_name":"Cortinovis","full_name":"Cortinovis, Emanuele","first_name":"Emanuele"}],"publisher":"Institute of Science and Technology Austria","date_published":"2026-06-15T00:00:00Z","month":"06","date_updated":"2026-06-15T23:00:03Z","department":[{"_id":"HeEd"}],"day":"15","abstract":[{"text":"A Rust library for analyzing dendritic structures using quadric matrices. This project provides efficient tools for representing dendritic trees, computing quadric error metrics, and visualizing eigenvalue distributions on hexagonal plots.\r\n\r\nThis library implements quadric-based geometric analysis of dendritic structures, commonly found in neuroscience applications. Key features include:\r\n\r\nTree data structures: Hierarchical vertex and edge representations for dendritic trees\r\nQuadric matrices: Computation of quadric error metrics for edges and vertices\r\nVisualisation: Hexagonal plot generation using NormPolar transformations\r\nInteractive tools: Desktop application with plotting capabilities","lang":"eng"}],"date_created":"2026-06-09T19:19:13Z","file_date_updated":"2026-06-15T08:14:24Z","keyword":["quadratics","mathematics","dendrites","geometry","topology"],"license":"https://opensource.org/licenses/MIT","title":"Quadrix","oa":1},{"publication":"Nano Letters","type":"journal_article","intvolume":"        26","citation":{"ista":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. 2026. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 26(22), 7429–7434.","short":"A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434.","chicago":"Gulyaev, Artem, Jyotisman Hazarika, Zhen-Fei Liu, and Latha Venkataraman. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>.","ieee":"A. Gulyaev, J. Hazarika, Z.-F. Liu, and L. Venkataraman, “A computationally efficient and accurate method for predicting conductance of single-molecule junctions,” <i>Nano Letters</i>, vol. 26, no. 22. American Chemical Society, pp. 7429–7434, 2026.","mla":"Gulyaev, Artem, et al. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” <i>Nano Letters</i>, vol. 26, no. 22, American Chemical Society, 2026, pp. 7429–7434, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>.","ama":"Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. 2026;26(22):7429–7434. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">10.1021/acs.nanolett.6c01462</a>","apa":"Gulyaev, A., Hazarika, J., Liu, Z.-F., &#38; Venkataraman, L. (2026). A computationally efficient and accurate method for predicting conductance of single-molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6c01462\">https://doi.org/10.1021/acs.nanolett.6c01462</a>"},"acknowledgement":"This work was supported primarily by the Institute of Science and Technology Austria. L.V. was supported in part by the National Science Foundation (No. NSF-DMR 2241180). Z.-F.L. was supported by an NSF CAREER Award, No. DMR-2044552 and an Alfred P. Sloan Research Fellowship, No. FG-2024-21750.","ddc":["540"],"external_id":{"pmid":["42223342"]},"author":[{"last_name":"Gulyaev","id":"83ed7901-7380-11f0-bf20-a0788d5e654d","full_name":"Gulyaev, Artem","first_name":"Artem"},{"last_name":"Hazarika","orcid":"0009-0007-2542-7878","id":"d87714c4-663d-11f0-bd06-caece19833e5","full_name":"Hazarika, Jyotisman","first_name":"Jyotisman"},{"last_name":"Liu","first_name":"Zhen-Fei","full_name":"Liu, Zhen-Fei"},{"last_name":"Venkataraman","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","full_name":"Venkataraman, Latha"}],"page":"7429–7434","quality_controlled":"1","doi":"10.1021/acs.nanolett.6c01462","_id":"21980","scopus_import":"1","pmid":1,"file_date_updated":"2026-06-16T09:11:35Z","volume":26,"title":"A computationally efficient and accurate method for predicting conductance of single-molecule junctions","language":[{"iso":"eng"}],"day":"01","abstract":[{"text":"Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance.","lang":"eng"}],"date_created":"2026-06-10T07:27:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"hybrid","file":[{"file_id":"22013","file_name":"2026_NanoLetters_Gulyaev.pdf","date_created":"2026-06-16T09:11:35Z","relation":"main_file","date_updated":"2026-06-16T09:11:35Z","creator":"dernst","access_level":"open_access","checksum":"897551374cac28e0db26dcb0b676b8e7","file_size":3362800,"content_type":"application/pdf","success":1}],"oa_version":"Published Version","year":"2026","issue":"22","status":"public","corr_author":"1","has_accepted_license":"1","PlanS_conform":"1","date_published":"2026-06-01T00:00:00Z","article_type":"letter_note","month":"06","publication_status":"published","date_updated":"2026-06-16T09:13:30Z","publisher":"American Chemical Society","oa":1,"department":[{"_id":"LaVe"},{"_id":"GradSch"}],"article_processing_charge":"Yes (via OA deal)"},{"status":"public","year":"2026","issue":"1","corr_author":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0022-1236"]},"OA_place":"publisher","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","file":[{"success":1,"access_level":"open_access","file_size":2503887,"checksum":"ee53d5e695f0df11e017c8c9242a2b04","content_type":"application/pdf","creator":"dernst","date_updated":"2026-01-05T13:05:47Z","relation":"main_file","date_created":"2026-01-05T13:05:47Z","file_name":"2026_JourFuncAnalysis_Cipolloni.pdf","file_id":"20947"}],"oa":1,"article_number":"111180","department":[{"_id":"LaEr"}],"article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","publication_status":"published","oaworkid":1,"date_updated":"2026-06-03T13:12:14Z","date_published":"2026-01-01T00:00:00Z","article_type":"original","month":"01","ec_funded":1,"publisher":"Elsevier","author":[{"first_name":"Giorgio","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László"},{"full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","orcid":"0000-0003-1559-1205","last_name":"Xu"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"_id":"20328","doi":"10.1016/j.jfa.2025.111180","type":"journal_article","publication":"Journal of Functional Analysis","intvolume":"       290","arxiv":1,"ddc":["510"],"external_id":{"arxiv":["2411.16572"],"isi":["001583178200001"],"oaworkid":["w4413883397"]},"acknowledgement":"Partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. Partially supported by National Key R&D Program of China No. 2024YFA1013503.","citation":{"ieee":"G. Cipolloni, L. Erdös, and Y. Xu, “Optimal decay of eigenvector overlap for non-Hermitian random matrices,” <i>Journal of Functional Analysis</i>, vol. 290, no. 1. Elsevier, 2026.","mla":"Cipolloni, Giorgio, et al. “Optimal Decay of Eigenvector Overlap for Non-Hermitian Random Matrices.” <i>Journal of Functional Analysis</i>, vol. 290, no. 1, 111180, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">10.1016/j.jfa.2025.111180</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Xu, Y. (2026). Optimal decay of eigenvector overlap for non-Hermitian random matrices. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">https://doi.org/10.1016/j.jfa.2025.111180</a>","ama":"Cipolloni G, Erdös L, Xu Y. Optimal decay of eigenvector overlap for non-Hermitian random matrices. <i>Journal of Functional Analysis</i>. 2026;290(1). doi:<a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">10.1016/j.jfa.2025.111180</a>","ista":"Cipolloni G, Erdös L, Xu Y. 2026. Optimal decay of eigenvector overlap for non-Hermitian random matrices. Journal of Functional Analysis. 290(1), 111180.","chicago":"Cipolloni, Giorgio, László Erdös, and Yuanyuan Xu. “Optimal Decay of Eigenvector Overlap for Non-Hermitian Random Matrices.” <i>Journal of Functional Analysis</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.jfa.2025.111180\">https://doi.org/10.1016/j.jfa.2025.111180</a>.","short":"G. Cipolloni, L. Erdös, Y. Xu, Journal of Functional Analysis 290 (2026)."},"volume":290,"file_date_updated":"2026-01-05T13:05:47Z","language":[{"iso":"eng"}],"title":"Optimal decay of eigenvector overlap for non-Hermitian random matrices","date_created":"2025-09-10T05:46:07Z","abstract":[{"lang":"eng","text":"We consider the standard overlap (math formular) of any bi-orthogonal family of left and right eigenvectors of a large random matrix X with centred i.i.d. entries and we prove that it decays as an inverse second power of the distance between the corresponding eigenvalues. This extends similar results for the complex Gaussian ensemble from Bourgade and Dubach [15], as well as Benaych-Georges and Zeitouni [13], to any i.i.d. matrix ensemble in both symmetry classes. As a main tool, we prove a two-resolvent local law for the Hermitisation of X uniformly in the spectrum with optimal decay rate and optimal dependence on the density near the spectral edge."}],"day":"01","isi":1,"scopus_import":"1"},{"department":[{"_id":"MaKw"}],"article_processing_charge":"Yes (via OA deal)","oa":1,"ec_funded":1,"publisher":"Elsevier","PlanS_conform":"1","article_type":"original","date_published":"2026-01-01T00:00:00Z","month":"01","date_updated":"2026-01-05T13:29:52Z","publication_status":"published","corr_author":"1","has_accepted_license":"1","year":"2026","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"hybrid","file":[{"success":1,"creator":"dernst","file_size":688924,"content_type":"application/pdf","checksum":"60676af4af4b3243ba187e7d65440d99","access_level":"open_access","date_updated":"2026-01-05T13:29:34Z","relation":"main_file","file_name":"2026_JourCombTheoryB_Christoph.pdf","date_created":"2026-01-05T13:29:34Z","file_id":"20953"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"issn":["0095-8956"],"eissn":["1096-0902"]},"abstract":[{"text":"We show that if n is odd and p>=Clog n/n, then with high probability Hamilton cycles in G(n,p) span its cycle space. More generally, we show this holds for a class of graphs satisfying certain natural pseudorandom properties. The proof is based on a novel idea of parity-switchers, which can be thought of as analogues of absorbers in the context of cycle spaces. As another application of our method, we show that Hamilton cycles in a near-Dirac graph G, that is, a graph G with odd n vertices and minimum degree n/2+C for sufficiently large constant C, span its cycle space.\r\n","lang":"eng"}],"day":"01","date_created":"2025-10-05T22:01:34Z","file_date_updated":"2026-01-05T13:29:34Z","volume":176,"title":"The Hamilton space of pseudorandom graphs","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"doi":"10.1016/j.jctb.2025.09.002","_id":"20422","author":[{"full_name":"Christoph, Micha","first_name":"Micha","last_name":"Christoph"},{"last_name":"Nenadov","first_name":"Rajko","full_name":"Nenadov, Rajko"},{"first_name":"Kalina H","full_name":"Petrova, Kalina H","id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","last_name":"Petrova"}],"page":"254-267","quality_controlled":"1","arxiv":1,"intvolume":"       176","citation":{"ista":"Christoph M, Nenadov R, Petrova KH. 2026. The Hamilton space of pseudorandom graphs. Journal of Combinatorial Theory Series B. 176, 254–267.","short":"M. Christoph, R. Nenadov, K.H. Petrova, Journal of Combinatorial Theory Series B 176 (2026) 254–267.","chicago":"Christoph, Micha, Rajko Nenadov, and Kalina H Petrova. “The Hamilton Space of Pseudorandom Graphs.” <i>Journal of Combinatorial Theory Series B</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">https://doi.org/10.1016/j.jctb.2025.09.002</a>.","ieee":"M. Christoph, R. Nenadov, and K. H. Petrova, “The Hamilton space of pseudorandom graphs,” <i>Journal of Combinatorial Theory Series B</i>, vol. 176. Elsevier, pp. 254–267, 2026.","mla":"Christoph, Micha, et al. “The Hamilton Space of Pseudorandom Graphs.” <i>Journal of Combinatorial Theory Series B</i>, vol. 176, Elsevier, 2026, pp. 254–67, doi:<a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">10.1016/j.jctb.2025.09.002</a>.","ama":"Christoph M, Nenadov R, Petrova KH. The Hamilton space of pseudorandom graphs. <i>Journal of Combinatorial Theory Series B</i>. 2026;176:254-267. doi:<a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">10.1016/j.jctb.2025.09.002</a>","apa":"Christoph, M., Nenadov, R., &#38; Petrova, K. H. (2026). The Hamilton space of pseudorandom graphs. <i>Journal of Combinatorial Theory Series B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jctb.2025.09.002\">https://doi.org/10.1016/j.jctb.2025.09.002</a>"},"acknowledgement":"This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Image 1 Part of this research was conducted while the author was at Department of Computer Science, ETH Zürich, Switzerland. This author was supported by grant no. CRSII5 173721 of the Swiss National Science Foundation.","ddc":["510"],"external_id":{"arxiv":["2402.01447"],"isi":["001585783400001"]},"type":"journal_article","publication":"Journal of Combinatorial Theory Series B"},{"author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","first_name":"Ranita"},{"last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano"},{"orcid":"0000-0003-0464-3823","last_name":"Draganov","first_name":"Ondrej","full_name":"Draganov, Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","last_name":"Saghafian"}],"page":"24-47","quality_controlled":"1","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"Mathematics, Computer Science"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"_id":"20456","doi":"10.1007/s00454-025-00778-7","type":"journal_article","publication":"Discrete and Computational Geometry","intvolume":"        75","arxiv":1,"ddc":["510"],"external_id":{"isi":["001584166900001"],"arxiv":["2212.03121"]},"acknowledgement":"The fourth author thanks Boris Aronov for insightful discussions on the size of the overlay of Voronoi tessellations. Open access funding provided by Institute of Science and Technology (IST Austria). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","citation":{"ista":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2026. On the size of chromatic Delaunay mosaics. Discrete and Computational Geometry. 75, 24–47.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “On the Size of Chromatic Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00778-7\">https://doi.org/10.1007/s00454-025-00778-7</a>.","short":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, Discrete and Computational Geometry 75 (2026) 24–47.","mla":"Biswas, Ranita, et al. “On the Size of Chromatic Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 24–47, doi:<a href=\"https://doi.org/10.1007/s00454-025-00778-7\">10.1007/s00454-025-00778-7</a>.","ieee":"R. Biswas, S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “On the size of chromatic Delaunay mosaics,” <i>Discrete and Computational Geometry</i>, vol. 75. Springer Nature, pp. 24–47, 2026.","apa":"Biswas, R., Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2026). On the size of chromatic Delaunay mosaics. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00778-7\">https://doi.org/10.1007/s00454-025-00778-7</a>","ama":"Biswas R, Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. On the size of chromatic Delaunay mosaics. <i>Discrete and Computational Geometry</i>. 2026;75:24-47. doi:<a href=\"https://doi.org/10.1007/s00454-025-00778-7\">10.1007/s00454-025-00778-7</a>"},"volume":75,"file_date_updated":"2026-01-05T13:21:20Z","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"15090"}]},"title":"On the size of chromatic Delaunay mosaics","date_created":"2025-10-12T22:01:26Z","day":"01","abstract":[{"text":"Given a locally finite set A⊆Rd and a coloring χ:A→{0,1,…,s}, we introduce the chromatic Delaunay mosaic of χ, which is a Delaunay mosaic in Rs+d that represents how points of different colors mingle. Our main results are bounds on the size of the chromatic Delaunay mosaic, in which we assume that d and s are constants. For example, if A is finite with n=#A, and the coloring is random, then the chromatic Delaunay mosaic has O(n⌈d/2⌉) cells in expectation. In contrast, for Delone sets and Poisson point processes in Rd, the expected number of cells within a closed ball is only a constant times the number of points in this ball. Furthermore, in R2 all colorings of a dense set of n points have chromatic Delaunay mosaics of size O(n). This encourages the use of chromatic Delaunay mosaics in applications.","lang":"eng"}],"isi":1,"scopus_import":"1","status":"public","year":"2026","corr_author":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"OA_place":"publisher","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","file":[{"success":1,"creator":"dernst","checksum":"0addb5c1b78142f9fb453bfa04695400","access_level":"open_access","content_type":"application/pdf","file_size":570922,"date_updated":"2026-01-05T13:21:20Z","relation":"main_file","file_name":"2026_DiscreteCompGeom_Biswas.pdf","date_created":"2026-01-05T13:21:20Z","file_id":"20952"}],"oa":1,"department":[{"_id":"HeEd"}],"article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","publication_status":"published","date_updated":"2026-01-05T13:21:56Z","month":"01","article_type":"original","date_published":"2026-01-01T00:00:00Z","ec_funded":1,"publisher":"Springer Nature"},{"scopus_import":"1","isi":1,"day":"01","abstract":[{"lang":"eng","text":"In his study of graph codes, Alon introduced the concept of the odd-Ramsey number of a family of graphs H in Kn, defined as the minimum number of colours needed to colour the edges of K so that every copy of a graph H E H intersects some colour class in an odd number of edges. In this paper, we focus on complete bipartite graphs. First, we completely resolve the problem when H is the family of all spanning complete bipartite graphs on n vertices. We then focus on its subfamilies, that is, {Kt,n-t : t E T} for a fixed set of integers T c [[n/2]]. We prove that the odd-Ramsey problem is equivalent to determining the maximum dimension of a linear binary code avoiding codewords of given weights, and leverage known results from coding theory to deduce asymptotically tight bounds in our setting. We conclude with bounds for the odd-Ramsey numbers of fixed (that is, non-spanning) complete bipartite subgraphs."}],"date_created":"2025-10-16T13:14:34Z","title":"Odd-Ramsey numbers of complete bipartite graphs","language":[{"iso":"eng"}],"file_date_updated":"2026-01-05T13:34:40Z","volume":131,"acknowledgement":"The authors would like to thank Gilles Zémor for a helpful clarification on [3], Deepak Bal and Patrick Bennett for bringing [25] to their attention, and both referees for several helpful comments.\r\nS.B.: Most of this research was conducted while the author was at the School of Mathematics, University of Birmingham, Birmingham, United Kingdom. The research leading to these results was supported by EPSRC, United Kingdom, grant no. EP/V048287/1 and by ERC Advanced Grants “GeoScape”, no. 882971 and “ERMiD”, no. 101054936. There are no additional data beyond that contained within the main manuscript.\r\nS.D.: Research supported by Taiwan NSTC grants 111-2115-M-002-009-MY2 and 113-2628-M-002-008-MY4.\r\nK.P.: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413. Parts of this research was conducted while K.P. was at the Department of Computer Science, ETH Zürich, Switzerland, supported by Swiss National Science Foundation, Switzerland , grant no. CRSII5 173721.","citation":{"ista":"Boyadzhiyska S, Das S, Lesgourgues T, Petrova KH. 2026. Odd-Ramsey numbers of complete bipartite graphs. European Journal of Combinatorics. 131, 104235.","short":"S. Boyadzhiyska, S. Das, T. Lesgourgues, K.H. Petrova, European Journal of Combinatorics 131 (2026).","chicago":"Boyadzhiyska, Simona, Shagnik Das, Thomas Lesgourgues, and Kalina H Petrova. “Odd-Ramsey Numbers of Complete Bipartite Graphs.” <i>European Journal of Combinatorics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">https://doi.org/10.1016/j.ejc.2025.104235</a>.","mla":"Boyadzhiyska, Simona, et al. “Odd-Ramsey Numbers of Complete Bipartite Graphs.” <i>European Journal of Combinatorics</i>, vol. 131, 104235, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">10.1016/j.ejc.2025.104235</a>.","ieee":"S. Boyadzhiyska, S. Das, T. Lesgourgues, and K. H. Petrova, “Odd-Ramsey numbers of complete bipartite graphs,” <i>European Journal of Combinatorics</i>, vol. 131. Elsevier, 2026.","ama":"Boyadzhiyska S, Das S, Lesgourgues T, Petrova KH. Odd-Ramsey numbers of complete bipartite graphs. <i>European Journal of Combinatorics</i>. 2026;131. doi:<a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">10.1016/j.ejc.2025.104235</a>","apa":"Boyadzhiyska, S., Das, S., Lesgourgues, T., &#38; Petrova, K. H. (2026). Odd-Ramsey numbers of complete bipartite graphs. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2025.104235\">https://doi.org/10.1016/j.ejc.2025.104235</a>"},"external_id":{"isi":["001573380700001"],"arxiv":["2410.05887"]},"ddc":["500"],"arxiv":1,"intvolume":"       131","type":"journal_article","publication":"European Journal of Combinatorics","doi":"10.1016/j.ejc.2025.104235","_id":"20482","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"quality_controlled":"1","author":[{"full_name":"Boyadzhiyska, Simona","first_name":"Simona","last_name":"Boyadzhiyska"},{"last_name":"Das","first_name":"Shagnik","full_name":"Das, Shagnik"},{"first_name":"Thomas","full_name":"Lesgourgues, Thomas","last_name":"Lesgourgues"},{"id":"554ff4e4-f325-11ee-b0c4-a10dbd523381","full_name":"Petrova, Kalina H","first_name":"Kalina H","last_name":"Petrova"}],"publisher":"Elsevier","ec_funded":1,"date_published":"2026-01-01T00:00:00Z","month":"01","article_type":"original","date_updated":"2026-01-05T13:34:48Z","publication_status":"published","PlanS_conform":"1","article_processing_charge":"Yes (via OA deal)","article_number":"104235","department":[{"_id":"MaKw"}],"oa":1,"file":[{"file_name":"2026_EuropJourCombinatorics_Boyadzhiyska.pdf","date_created":"2026-01-05T13:34:40Z","relation":"main_file","file_id":"20954","creator":"dernst","checksum":"52883daa217398396cbf9b8ad9ddae92","file_size":563029,"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2026-01-05T13:34:40Z"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"OA_type":"hybrid","OA_place":"publisher","publication_identifier":{"issn":["0195-6698"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","has_accepted_license":"1","year":"2026","status":"public"},{"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41535-026-00901-8","open_access":"1"}],"title":"Linear magneto-birefringence as a probe of altermagnetism","date_created":"2026-03-11T10:40:08Z","day":"30","abstract":[{"lang":"eng","text":"Altermagnets are a class of collinear magnets that exhibit non-relativistic spin splitting (NRSS) of electronic bands in the absence of net magnetization. Their potential to generate large spin polarization without spin-orbit coupling has created strong interest in probes that access the underlying order parameter directly. In this Perspective, we show that linear magneto-birefringence (LMB) provides a natural and broadly applicable route to detecting altermagnetic order. Building on the correspondence between the momentum-space structure of NRSS and the ferroic ordering of magnetic multipoles in real space, we demonstrate how $d$-wave and $g$-wave NRSS textures yield distinct LMB responses. We present a symmetry-based framework that identifies the optical geometries and field configurations required to isolate specific multipole components, enabling domain imaging and providing benchmarks for theoretical models of LMB."}],"author":[{"last_name":"Sunko","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","first_name":"Veronika","full_name":"Sunko, Veronika"},{"last_name":"Orenstein","first_name":"J.","full_name":"Orenstein, J."}],"_id":"21437","doi":"10.1038/s41535-026-00901-8","publication":"npj Quantum Materials","type":"journal_article","arxiv":1,"ddc":["530"],"external_id":{"arxiv":["2511.16421"]},"citation":{"chicago":"Sunko, Veronika, and J. Orenstein. “Linear Magneto-Birefringence as a Probe of Altermagnetism.” <i>Npj Quantum Materials</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41535-026-00901-8\">https://doi.org/10.1038/s41535-026-00901-8</a>.","short":"V. Sunko, J. Orenstein, Npj Quantum Materials (2026).","ista":"Sunko V, Orenstein J. 2026. Linear magneto-birefringence as a probe of altermagnetism. npj Quantum Materials.","apa":"Sunko, V., &#38; Orenstein, J. (2026). Linear magneto-birefringence as a probe of altermagnetism. <i>Npj Quantum Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41535-026-00901-8\">https://doi.org/10.1038/s41535-026-00901-8</a>","ama":"Sunko V, Orenstein J. Linear magneto-birefringence as a probe of altermagnetism. <i>npj Quantum Materials</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41535-026-00901-8\">10.1038/s41535-026-00901-8</a>","ieee":"V. Sunko and J. Orenstein, “Linear magneto-birefringence as a probe of altermagnetism,” <i>npj Quantum Materials</i>. Springer Nature, 2026.","mla":"Sunko, Veronika, and J. Orenstein. “Linear Magneto-Birefringence as a Probe of Altermagnetism.” <i>Npj Quantum Materials</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41535-026-00901-8\">10.1038/s41535-026-00901-8</a>."},"acknowledgement":"We thank Nicola Spaldin and Marc Vila for valuable discussions. J.O. received support from the Quantum Materials (KC2202) program under the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05CH11231, and the Gordon and Betty Moore Foundation's EPiQS Initiative through Grant GBMF4537 to J.O. at UC Berkeley.","oa":1,"department":[{"_id":"VeSu"}],"article_processing_charge":"Yes","publication_status":"epub_ahead","date_updated":"2026-06-24T10:31:05Z","date_published":"2026-05-30T00:00:00Z","article_type":"original","month":"05","publisher":"Springer Nature","status":"public","year":"2026","has_accepted_license":"1","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2397-4648"]},"OA_place":"publisher","OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"OA_type":"gold","file":[{"relation":"main_file","file_name":"2026_NatureComm_Svoboda.pdf","date_created":"2026-06-24T06:50:24Z","file_id":"22136","success":1,"creator":"dernst","checksum":"b660048bb271f24d6763803e247d5c32","content_type":"application/pdf","access_level":"open_access","file_size":1068919,"date_updated":"2026-06-24T06:50:24Z"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"eissn":["2041-1723"]},"corr_author":"1","researchdata_availability":"no","has_accepted_license":"1","year":"2026","status":"public","dataavailabilitystatement":"Correspondence and requests for materials should be addressed to Krishnendu Chatterjee.","das_tickbox":"0","ec_funded":1,"publisher":"Springer Nature","supplementarymaterial":"yes","article_type":"original","date_published":"2026-12-01T00:00:00Z","month":"12","date_updated":"2026-06-24T07:53:53Z","publication_status":"published","department":[{"_id":"KrCh"}],"article_number":"5325","article_processing_charge":"Yes","oa":1,"intvolume":"        17","citation":{"apa":"Svoboda, J., Nemati, H., Tkadlec, J., Kaveh, K., &#38; Chatterjee, K. (2026). The effect of the fitness gradient on fixation probability. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-71777-2\">https://doi.org/10.1038/s41467-026-71777-2</a>","ama":"Svoboda J, Nemati H, Tkadlec J, Kaveh K, Chatterjee K. The effect of the fitness gradient on fixation probability. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-71777-2\">10.1038/s41467-026-71777-2</a>","mla":"Svoboda, Jakub, et al. “The Effect of the Fitness Gradient on Fixation Probability.” <i>Nature Communications</i>, vol. 17, 5325, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-71777-2\">10.1038/s41467-026-71777-2</a>.","ieee":"J. Svoboda, H. Nemati, J. Tkadlec, K. Kaveh, and K. Chatterjee, “The effect of the fitness gradient on fixation probability,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","chicago":"Svoboda, Jakub, Hossein Nemati, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “The Effect of the Fitness Gradient on Fixation Probability.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-71777-2\">https://doi.org/10.1038/s41467-026-71777-2</a>.","short":"J. Svoboda, H. Nemati, J. Tkadlec, K. Kaveh, K. Chatterjee, Nature Communications 17 (2026).","ista":"Svoboda J, Nemati H, Tkadlec J, Kaveh K, Chatterjee K. 2026. The effect of the fitness gradient on fixation probability. Nature Communications. 17, 5325."},"acknowledgement":"J.S. and K.C. were supported by the European Research Council (ERC)\r\nCoG 863818 (ForM-SMArt) and Austrian Science Fund (FWF) 10.55776/\r\nCOE12. J.T. was supported by GAČR grant 25-17377S and by Charles\r\nUniv. projects UNCE 24/SCI/008 and PRIMUS 24/SCI/012.","ddc":["000"],"external_id":{"pmid":["41997932"]},"publication":"Nature Communications","type":"journal_article","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1038/s41467-026-71777-2","_id":"22101","author":[{"orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"first_name":"Hossein","full_name":"Nemati, Hossein","last_name":"Nemati"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef"},{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"quality_controlled":"1","pmid":1,"scopus_import":"1","day":"01","abstract":[{"text":"Evolutionary biology examines how the genetic and phenotypic composition\r\nof populations changes over time. An important goal is to determine the\r\nfixation probability of a single advantageous mutant that arises in a homogeneous\r\npopulation of N residents. Many real populations experience environmental\r\ngradients that cause mutations to be beneficial in some spatial\r\nregions but harmful in others. Here, we study the fixation probability of a\r\nmutant placed on a simple one-dimensional spatial structure that experiences\r\nsuch a gradient. The mutant’s fitness varies linearly from1 − s to 1 + s, whereas\r\nthe resident fitness is constant and equal to 1. The existing literature suggests\r\nthat such heterogeneity in the mutant’s fitness should lead to a decrease in its\r\nfixation probability. However, in this work, we find that small, non-negligible\r\ngradients (s < 1=√N) substantially increase the fixation probability,while larger\r\ngradients (s > (log N)/√N) substantially decrease it.Moreover, we quantify the\r\nstrength of this phenomenon analytically and we precisely delimit the range of\r\nthe gradients for which it occurs. Our computer simulations closely match\r\nthose findings. Altogether, our results indicate that subjecting a simple\r\npopulation structure to natural environmental conditions can produce strong\r\ncounterintuitive effects.","lang":"eng"}],"date_created":"2026-06-21T22:02:59Z","file_date_updated":"2026-06-24T06:50:24Z","volume":17,"title":"The effect of the fitness gradient on fixation probability","DOAJ_listed":"1","language":[{"iso":"eng"}]},{"intvolume":"         5","citation":{"mla":"Cano Cordoba, Filip. “Explaining Decisions One Conversation at a Time: Opportunities and Risks of LLMs as Explainability Assistants.” <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, vol. 5, Science and Technology Publications, 2026, pp. 4689–96, doi:<a href=\"https://doi.org/10.5220/0014483200004052\">10.5220/0014483200004052</a>.","ieee":"F. Cano Cordoba, “Explaining decisions one conversation at a time: Opportunities and risks of LLMs as explainability assistants,” in <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, Marbella, Spain, 2026, vol. 5, pp. 4689–4696.","ama":"Cano Cordoba F. Explaining decisions one conversation at a time: Opportunities and risks of LLMs as explainability assistants. In: <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>. Vol 5. Science and Technology Publications; 2026:4689-4696. doi:<a href=\"https://doi.org/10.5220/0014483200004052\">10.5220/0014483200004052</a>","apa":"Cano Cordoba, F. (2026). Explaining decisions one conversation at a time: Opportunities and risks of LLMs as explainability assistants. In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i> (Vol. 5, pp. 4689–4696). Marbella, Spain: Science and Technology Publications. <a href=\"https://doi.org/10.5220/0014483200004052\">https://doi.org/10.5220/0014483200004052</a>","ista":"Cano Cordoba F. 2026. Explaining decisions one conversation at a time: Opportunities and risks of LLMs as explainability assistants. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 5, 4689–4696.","short":"F. Cano Cordoba, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 4689–4696.","chicago":"Cano Cordoba, Filip. “Explaining Decisions One Conversation at a Time: Opportunities and Risks of LLMs as Explainability Assistants.” In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, 5:4689–96. Science and Technology Publications, 2026. <a href=\"https://doi.org/10.5220/0014483200004052\">https://doi.org/10.5220/0014483200004052</a>."},"acknowledgement":"This work has been supported by the European Research Council under Grant No.: ERC-2020-AdG\r\n101020093. LLM–based tools have been used as\r\nwriting assistance to help improve presentation.\r\n","type":"conference","publication":"Proceedings of the 18th International Conference on Agents and Artificial Intelligence","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"_id":"22103","doi":"10.5220/0014483200004052","author":[{"last_name":"Cano Cordoba","orcid":"0000-0002-0783-904X","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","full_name":"Cano Cordoba, Filip","first_name":"Filip"}],"page":"4689-4696","quality_controlled":"1","scopus_import":"1","date_created":"2026-06-21T22:03:00Z","day":"01","abstract":[{"lang":"eng","text":"Modern AI systems increasingly rely on opaque, highly complex models whose inner workings remain inaccessible even to experts. This opacity creates challenges for trust, accountability, and compliance with\r\nemerging regulatory expectations such as the “right to an explanation”. While traditional explainability methods—feature attributions, counterfactuals, surrogate models—and interpretable model classes provide valuable insights for engineers, they often fall short of delivering the contextual, conversational explanations that\r\nreal users expect. Large Language Models (LLMs) offer a promising new avenue for explanation due to their\r\nability to engage interactively, adapt to user needs, and translate technical outputs into more accessible reasoning. However, their tendencies toward hallucination, conflict avoidance, and oversimplification introduce\r\nserious risks when used as explanatory agents. This paper analyzes these opportunities and limitations, examines verification strategies for ensuring explanation fidelity, and situates LLM-generated explanations within\r\nbroader concerns about public trust. The paper concludes by outlining best practices and future research directions for building robust, verifiable, and human-aligned explanation systems."}],"keyword":["Explainable AI","Large Language Models","Trust in AI"],"volume":5,"main_file_link":[{"open_access":"1","url":"https://filipcano.org/files/icaart26llm.pdf"}],"language":[{"iso":"eng"}],"title":"Explaining decisions one conversation at a time: Opportunities and risks of LLMs as explainability assistants","OA_type":"green","oa_version":"Accepted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2184-3589"],"isbn":["9789897587962"],"eissn":["2184-433X"]},"OA_place":"repository","researchdata_availability":"no","corr_author":"1","status":"public","year":"2026","ec_funded":1,"das_tickbox":"0","publisher":"Science and Technology Publications","supplementarymaterial":"no","date_updated":"2026-06-24T08:37:00Z","publication_status":"published","month":"04","date_published":"2026-04-01T00:00:00Z","department":[{"_id":"ToHe"}],"conference":{"end_date":"2026-03-08","location":"Marbella, Spain","start_date":"2026-03-05","name":"ICAART: International Conference on Agents and Artificial Intelligence"},"article_processing_charge":"No","oa":1},{"author":[{"last_name":"Becker","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","full_name":"Becker, Lea Marie"},{"full_name":"Fu, Haohao","first_name":"Haohao","last_name":"Fu"},{"last_name":"Tatman","full_name":"Tatman, Benjamin","first_name":"Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"},{"last_name":"Dreydoppel","full_name":"Dreydoppel, Matthias","first_name":"Matthias"},{"last_name":"Kapitonova","full_name":"Kapitonova, Anna","first_name":"Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471"},{"full_name":"Balazs, Daniel","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"full_name":"Weininger, Ulrich","first_name":"Ulrich","last_name":"Weininger"},{"last_name":"Engilberge","full_name":"Engilberge, Sylvain","first_name":"Sylvain"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul"}],"quality_controlled":"1","project":[{"grant_number":"26777","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"_id":"22105","doi":"10.1038/s41557-026-02155-0","publication":"Nature Chemistry","type":"journal_article","external_id":{"pmid":["42271006"]},"ddc":["540"],"citation":{"ista":"Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry.","short":"L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U. Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry (2026).","chicago":"Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot, and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>.","mla":"Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>.","ieee":"L. M. Becker <i>et al.</i>, “Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes,” <i>Nature Chemistry</i>. Springer Nature, 2026.","ama":"Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>","apa":"Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs, D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>"},"acknowledgement":"We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged for providing beamtime through its In-House Research programme. We thank S. Falkner for assistance with constructing the structural model of the IgG:GB1 complex. We thank J. Lewandowski for providing feedback on the paper and granting access to backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant number PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272 ‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science and Technology (IST Austria).","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"20641"},{"status":"public","id":"21145","relation":"research_data"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41557-026-02155-0"}],"title":"Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes","date_created":"2026-06-21T22:03:01Z","abstract":[{"text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein–protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions.","lang":"eng"}],"day":"10","scopus_import":"1","pmid":1,"year":"2026","status":"public","researchdata_availability":"yes","has_accepted_license":"1","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["17554330"],"eissn":["17554349"]},"OA_place":"publisher","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","oa":1,"department":[{"_id":"PaSc"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","supplementarymaterial":"yes","date_updated":"2026-06-24T08:47:58Z","publication_status":"epub_ahead","date_published":"2026-06-10T00:00:00Z","article_type":"original","month":"06","das_tickbox":"1","dataavailabilitystatement":"The cryo and room-temperature crystal structures of GB1QDD are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the access code 53330. NMR spectra, analysis scripts and raw data are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files to reproduce the enhanced-sampling MD simulations are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121.","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}]},{"corr_author":"1","has_accepted_license":"1","status":"public","year":"2026","file":[{"date_created":"2026-02-05T13:52:37Z","file_name":"README.txt","relation":"table_of_contents","file_id":"21146","content_type":"text/plain","checksum":"02a419cce8cea450bc952f35488d2df5","access_level":"open_access","file_size":4263,"creator":"lbecker","date_updated":"2026-02-05T13:52:37Z"},{"date_created":"2026-02-05T13:52:41Z","file_name":"Research_Data.zip","relation":"main_file","file_id":"21147","checksum":"b0b82b1aa73985b0b308a3fa52d21aea","content_type":"application/zip","access_level":"open_access","file_size":50647107,"creator":"lbecker","success":1,"date_updated":"2026-02-05T13:52:41Z"}],"oa_version":"Published Version","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"oa":1,"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","month":"02","date_published":"2026-02-09T00:00:00Z","contributor":[{"first_name":"Haohao","contributor_type":"researcher","last_name":"Fu"},{"first_name":"Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f","last_name":"Tatman","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Dreydoppel","first_name":"Matthias"},{"first_name":"Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","contributor_type":"researcher","last_name":"Kapitonova"},{"orcid":"0000-0001-7597-043X","contributor_type":"researcher","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Ulrich","last_name":"Weininger","contributor_type":"researcher"},{"first_name":"Sylvain","contributor_type":"researcher","last_name":"Engilberge"}],"date_updated":"2026-06-24T08:47:57Z","doi":"10.15479/AT-ISTA-21145","_id":"21145","project":[{"_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","grant_number":"26777","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"author":[{"last_name":"Becker","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie","first_name":"Lea Marie"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"}],"acknowledgement":"We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.","citation":{"ieee":"L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026.","mla":"Becker, Lea Marie, et al. <i>Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>.","ama":"Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>","apa":"Becker, L. M., Schanda, P., &#38; Chipot, C. (2026). Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>","ista":"Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>.","short":"L.M. Becker, P. Schanda, C. Chipot, (2026).","chicago":"Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>."},"ddc":["572"],"type":"research_data","abstract":[{"lang":"eng","text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. "}],"day":"09","date_created":"2026-02-05T13:54:39Z","title":"Additional Data for \"Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes\"","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"20641"},{"status":"public","id":"22105","relation":"used_in_publication"}]},"file_date_updated":"2026-02-05T13:52:41Z"},{"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959774192"]},"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","alternative_title":["LIPIcs"],"file":[{"date_updated":"2026-06-29T06:55:23Z","success":1,"checksum":"c661f016d3861a1c1b590b87a744d087","file_size":1231914,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_id":"22149","relation":"main_file","date_created":"2026-06-29T06:55:23Z","file_name":"2026_LIPIcsFORC_Kalinin.pdf"}],"OA_type":"gold","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","year":"2026","has_accepted_license":"1","corr_author":"1","researchdata_availability":"no","date_updated":"2026-06-29T06:56:34Z","publication_status":"published","month":"06","date_published":"2026-06-01T00:00:00Z","supplementarymaterial":"no","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"das_tickbox":"0","oa":1,"article_processing_charge":"No","article_number":"2:1-2:21","conference":{"start_date":"2026-06-03","name":"FORC: Symposium on Foundations of Responsible Computing","end_date":"2026-06-05","location":"Cambridge, MA; United States"},"department":[{"_id":"ChLa"},{"_id":"GradSch"},{"_id":"MoHe"}],"publication":"7th Symposium on Foundations of Responsible Computing","type":"conference","ddc":["000"],"external_id":{"arxiv":["2511.17994"]},"acknowledgement":"We thank Rasmus Pagh, Christoph Lampert and Jalaj Upadhyay for valuable\r\ncomments on an early draft. We thank Ryan Mckenna for a fruitful discussion on the experiment\r\ndesign. We thank Antti Honkela for sharing insights on learning rate scheduling and DP.\r\nNikita P. Kalinin: Funded in part by the Austrian Science Fund (FWF) [10.55776/COE12].\r\nJoel Daniel Andersson: Funded by the European Union. Views and opinions expressed are however\r\nthose of the author(s) only and do not necessarily reflect those of the European Union or the European\r\nResearch Council Executive Agency. Neither the European Union nor the granting authority can be\r\nheld responsible for them. This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct,\r\nNo. 101019564). Additional funding by Providentia, a Data Science Distinguished Investigator grant\r\nfrom Novo Nordisk Fonden, with additional support from VILLUM Investigator grant 54451.\r\n","citation":{"apa":"Kalinin, N., &#38; Andersson, J. D. (2026). Learning rate scheduling with matrix factorization for private training. In <i>7th Symposium on Foundations of Responsible Computing</i> (Vol. 368). Cambridge, MA; United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FORC.2026.2\">https://doi.org/10.4230/LIPIcs.FORC.2026.2</a>","ama":"Kalinin N, Andersson JD. Learning rate scheduling with matrix factorization for private training. In: <i>7th Symposium on Foundations of Responsible Computing</i>. Vol 368. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2026. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FORC.2026.2\">10.4230/LIPIcs.FORC.2026.2</a>","mla":"Kalinin, Nikita, and Joel D. Andersson. “Learning Rate Scheduling with Matrix Factorization for Private Training.” <i>7th Symposium on Foundations of Responsible Computing</i>, vol. 368, 2:1-2:21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2026, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FORC.2026.2\">10.4230/LIPIcs.FORC.2026.2</a>.","ieee":"N. Kalinin and J. D. Andersson, “Learning rate scheduling with matrix factorization for private training,” in <i>7th Symposium on Foundations of Responsible Computing</i>, Cambridge, MA; United States, 2026, vol. 368.","chicago":"Kalinin, Nikita, and Joel D Andersson. “Learning Rate Scheduling with Matrix Factorization for Private Training.” In <i>7th Symposium on Foundations of Responsible Computing</i>, Vol. 368. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2026. <a href=\"https://doi.org/10.4230/LIPIcs.FORC.2026.2\">https://doi.org/10.4230/LIPIcs.FORC.2026.2</a>.","short":"N. Kalinin, J.D. Andersson, in:, 7th Symposium on Foundations of Responsible Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2026.","ista":"Kalinin N, Andersson JD. 2026. Learning rate scheduling with matrix factorization for private training. 7th Symposium on Foundations of Responsible Computing. FORC: Symposium on Foundations of Responsible Computing, LIPIcs, vol. 368, 2:1-2:21."},"intvolume":"       368","arxiv":1,"quality_controlled":"1","author":[{"last_name":"Kalinin","id":"4b14526e-14d2-11ed-ba64-c14c9553d137","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"last_name":"Andersson","id":"4a893819-d954-11f0-89b1-e360bad9ccc5","first_name":"Joel D","full_name":"Andersson, Joel D"}],"_id":"22146","doi":"10.4230/LIPIcs.FORC.2026.2","project":[{"call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"}],"scopus_import":"1","language":[{"iso":"eng"}],"title":"Learning rate scheduling with matrix factorization for private training","volume":368,"keyword":["differential privacy","machine learning","matrix factorization"],"file_date_updated":"2026-06-29T06:55:23Z","date_created":"2026-06-28T22:01:34Z","day":"01","abstract":[{"lang":"eng","text":"We study differentially private model training with stochastic gradient descent under learning rate scheduling and correlated noise. Although correlated noise, in particular via matrix factorizations, has been shown to improve accuracy, prior theoretical work focused primarily on the prefix-sum workload. That workload assumes a constant learning rate, whereas in practice learning rate schedules are widely used to accelerate training and improve convergence. We close this gap by deriving general upper and lower bounds for a broad class of learning rate schedules in both single- and multi-epoch settings. Building on these results, we propose a learning-rate-aware factorization that achieves improvements over prefix-sum factorizations under both MaxSE and MeanSE error metrics. Our theoretical analysis yields memory-efficient constructions suitable for practical deployment, and experiments on CIFAR-10 and IMDB datasets confirm that schedule-aware factorizations improve accuracy in private training."}]}]