--- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '22957' abstract: - lang: eng text: Linguistic inequality remains a silent barrier in contemporary science, particularly in rapidly evolving and interdisciplinary fields such as bioinformatics. This article examines how the Spanish-speaking community has responded to this gap through the creation of the Simposio de Estudiantes Hispanohablantes de Bioinformática y Biología Computacional (SEH2Bioinfo), a collective initiative that transforms language into a tool for inclusion and collaboration. Drawing on a historical review of the use of Spanish in scientific communication and an analysis of the two editions of SEH2Bioinfo (2022 and 2025), complemented by surveys of more than 1500 participants, we explore the effects of language on confidence, participation, and academic visibility. The findings show that Spanish can serve as a space for training and mentorship without compromising rigor, while simultaneously strengthening international networks and promoting open science. The growth of SEH2Bioinfo, its collaborative approach, and its intercontinental reach establish the symposium as a model for linguistic equity in scientific practice. Its experience demonstrates that expanding linguistic diversity in bioinformatics is not only possible but essential to building a global scientific community that is fairer, more connected, and representative. acknowledgement: "We acknowledge the sponsors who made the SEH2Bioinfo possible, the organizers from the various Spanish-speaking RSGs, and\r\nthe collaborators who contributed to dissemination, logistics,\r\nand other essential tasks for its execution. G.J.O.-O. thanks the\r\nFONDECYT Postdoctoral Project No. 3250793 for financial support. G.J.O.-O. also expresses gratitude to Valentina Luza: “May\r\nher passion for science communication keep inspiring new generations, myself included, to infinity and beyond!” R.G.P.\r\nthanks the Argentinian public university education system as an\r\nelement of social ascendance and democratization of professional opportunities." article_number: vbag182 article_processing_charge: Yes article_type: original author: - first_name: Carla L full_name: Padilla Franzotti, Carla L last_name: Padilla Franzotti - first_name: Gabriel J full_name: Olguín-Orellana, Gabriel J last_name: Olguín-Orellana - first_name: Nicolas full_name: Palopoli, Nicolas last_name: Palopoli - first_name: Sebastián full_name: Urquiza-Zurich, Sebastián last_name: Urquiza-Zurich - first_name: Adrian full_name: Garcia-Moreno, Adrian last_name: Garcia-Moreno - first_name: Sara full_name: Monzón, Sara last_name: Monzón - first_name: Mónica full_name: Cabrera-Pasadas, Mónica last_name: Cabrera-Pasadas - first_name: Irene full_name: Soler Sáez, Irene last_name: Soler Sáez - first_name: Carla full_name: Perpiñá-Clérigues, Carla last_name: Perpiñá-Clérigues - first_name: Rafael J full_name: Puche Quiñonez, Rafael J last_name: Puche Quiñonez - first_name: Jennifer full_name: Vélez Segura, Jennifer last_name: Vélez Segura - first_name: Jose Abel full_name: Lovaco-Flores, Jose Abel last_name: Lovaco-Flores - first_name: Cleidy M full_name: Osorio Mogollón, Cleidy M last_name: Osorio Mogollón - first_name: Eva M full_name: Esquinas-Román, Eva M last_name: Esquinas-Román - first_name: Maria C full_name: Miserendino, Maria C id: 273e0cbd-72f0-11ef-b75a-f9f932e292fa last_name: Miserendino - first_name: Pradeep full_name: Eranti, Pradeep last_name: Eranti - first_name: Ana full_name: Castillo-Orozco, Ana last_name: Castillo-Orozco - first_name: Yesid full_name: Cuesta-Astroz, Yesid last_name: Cuesta-Astroz - first_name: R Gonzalo full_name: Parra, R Gonzalo last_name: Parra citation: ama: 'Padilla Franzotti CL, Olguín-Orellana GJ, Palopoli N, et al. Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. Bioinformatics Advances. 2026;6(1). doi:10.1093/bioadv/vbag182' apa: 'Padilla Franzotti, C. L., Olguín-Orellana, G. J., Palopoli, N., Urquiza-Zurich, S., Garcia-Moreno, A., Monzón, S., … Parra, R. G. (2026). Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. Bioinformatics Advances. Oxford University Press. https://doi.org/10.1093/bioadv/vbag182' chicago: 'Padilla Franzotti, Carla L, Gabriel J Olguín-Orellana, Nicolas Palopoli, Sebastián Urquiza-Zurich, Adrian Garcia-Moreno, Sara Monzón, Mónica Cabrera-Pasadas, et al. “Bioinformatics in Español: Expanding Open, Diverse, and Collaborative Science through SEH2Bioinfo.” Bioinformatics Advances. Oxford University Press, 2026. https://doi.org/10.1093/bioadv/vbag182.' ieee: 'C. L. Padilla Franzotti et al., “Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo,” Bioinformatics Advances, vol. 6, no. 1. Oxford University Press, 2026.' ista: 'Padilla Franzotti CL, Olguín-Orellana GJ, Palopoli N, Urquiza-Zurich S, Garcia-Moreno A, Monzón S, Cabrera-Pasadas M, Soler Sáez I, Perpiñá-Clérigues C, Puche Quiñonez RJ, Vélez Segura J, Lovaco-Flores JA, Osorio Mogollón CM, Esquinas-Román EM, Miserendino MC, Eranti P, Castillo-Orozco A, Cuesta-Astroz Y, Parra RG. 2026. Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. Bioinformatics Advances. 6(1), vbag182.' mla: 'Padilla Franzotti, Carla L., et al. “Bioinformatics in Español: Expanding Open, Diverse, and Collaborative Science through SEH2Bioinfo.” Bioinformatics Advances, vol. 6, no. 1, vbag182, Oxford University Press, 2026, doi:10.1093/bioadv/vbag182.' short: C.L. Padilla Franzotti, G.J. Olguín-Orellana, N. Palopoli, S. Urquiza-Zurich, A. Garcia-Moreno, S. Monzón, M. Cabrera-Pasadas, I. Soler Sáez, C. Perpiñá-Clérigues, R.J. Puche Quiñonez, J. Vélez Segura, J.A. Lovaco-Flores, C.M. Osorio Mogollón, E.M. Esquinas-Román, M.C. Miserendino, P. Eranti, A. Castillo-Orozco, Y. Cuesta-Astroz, R.G. Parra, Bioinformatics Advances 6 (2026). das_tickbox: '1' dataavailabilitystatement: "The data underlying this article, including the abstract books for\r\nthe first and second editions of the SEH2Bioinfo symposia, are\r\navailable in Zenodo at https://doi.org/10.5281/zenodo.6603621\r\nand https://doi.org/10.5281/zenodo.1,54,46,570, respectively." date_created: 2026-09-17T11:06:17Z date_published: 2026-08-06T00:00:00Z date_updated: 2026-10-01T08:59:32Z day: '06' ddc: - '570' department: - _id: PaSc - _id: GradSch doi: 10.1093/bioadv/vbag182 external_id: pmid: - '42577783' file: - access_level: open_access checksum: 8885b0531a655103c46899b2f935b0db content_type: application/pdf creator: dernst date_created: 2026-10-01T08:55:00Z date_updated: 2026-10-01T08:55:00Z file_id: '23016' file_name: 2026_BioinformaticsAdvances_Franzotti.pdf file_size: 1359968 relation: main_file success: 1 file_date_updated: 2026-10-01T08:55:00Z fulldoi: https://doi.org/10.1093/bioadv/vbag182 has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Bioinformatics Advances publication_identifier: eissn: - 2635-0041 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/bioadv/vbag271 researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: 'Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '22958' abstract: - lang: eng text: "We propose a sensing scheme for detecting weak forces that achieves sensitivity scaling proportional to the number of individual sensors without relying on entanglement or other non-classical resources. Our scheme utilizes coherent averaging across a chain of \r\n optomechanical cavities, unidirectionally coupled via a laser beam. As the beam passes through the cavities, it accumulates phase shifts induced by a common external force acting on the mechanical elements. Remarkably, this fully classical approach achieves the sensitivity scaling typically associated with quantum-enhanced protocols, providing a robust and experimentally feasible route to precision sensing. Potential applications range from high-sensitivity gravitational field measurements at the Large Hadron Collider to probing dark matter interactions and detecting gravitational waves. This work opens a new pathway for leveraging coherent light-matter interactions for force sensing." acknowledgement: 'We thank Germain Tobar, Navdeep Arya, Magdalena Zych, Teodor Strömberg and Onur Hosten for useful discussions. M M M acknowledges support from the Walter Benjamin Programme (Project Number 510053905) and from the Austrian Science Fund (FWF) [10.55776/COE1]. DB acknowledges funding by the EU EIC Pathfinder project QuCoM (101046973). D R acknowledges funding by the Federal Ministry of Education and Research of Germany in the project ‘Open6GHub’ (Grant Number: 16KISK016), financial support from EPSRC (Engineering & Physical Sciences Research Council, United Kingdom) Grant Number EP/X009467/1, and support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2123 QuantumFrontiers - 390837967.' article_number: '084505' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Marta M full_name: Marchese, Marta M id: fdac3bd4-d1c1-11ef-aaa4-fad05dc21577 last_name: Marchese - first_name: Daniel full_name: Braun, Daniel last_name: Braun - first_name: Stefan full_name: Nimmrichter, Stefan last_name: Nimmrichter - first_name: Dennis full_name: Rätzel, Dennis last_name: Rätzel citation: ama: Marchese MM, Braun D, Nimmrichter S, Rätzel D. Cascaded optomechanical sensing for small signals. New Journal of Physics. 2026;28(8). doi:10.1088/1367-2630/ae8b16 apa: Marchese, M. M., Braun, D., Nimmrichter, S., & Rätzel, D. (2026). Cascaded optomechanical sensing for small signals. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ae8b16 chicago: Marchese, Marta M, Daniel Braun, Stefan Nimmrichter, and Dennis Rätzel. “Cascaded Optomechanical Sensing for Small Signals.” New Journal of Physics. IOP Publishing, 2026. https://doi.org/10.1088/1367-2630/ae8b16. ieee: M. M. Marchese, D. Braun, S. Nimmrichter, and D. Rätzel, “Cascaded optomechanical sensing for small signals,” New Journal of Physics, vol. 28, no. 8. IOP Publishing, 2026. ista: Marchese MM, Braun D, Nimmrichter S, Rätzel D. 2026. Cascaded optomechanical sensing for small signals. New Journal of Physics. 28(8), 084505. mla: Marchese, Marta M., et al. “Cascaded Optomechanical Sensing for Small Signals.” New Journal of Physics, vol. 28, no. 8, 084505, IOP Publishing, 2026, doi:10.1088/1367-2630/ae8b16. short: M.M. Marchese, D. Braun, S. Nimmrichter, D. Rätzel, New Journal of Physics 28 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All data that support the findings of this study are included within the article (and any supplementary files). date_created: 2026-09-17T11:06:23Z date_published: 2026-08-13T00:00:00Z date_updated: 2026-10-01T09:19:39Z day: '13' ddc: - '530' department: - _id: OnHo doi: 10.1088/1367-2630/ae8b16 external_id: arxiv: - '2602.08981' file: - access_level: open_access checksum: b932d9f4bac1a2f6777e41d884b7b703 content_type: application/pdf creator: dernst date_created: 2026-10-01T09:17:19Z date_updated: 2026-10-01T09:17:19Z file_id: '23018' file_name: 2026_NewJourPhysics_Marchese.pdf file_size: 799610 relation: main_file success: 1 file_date_updated: 2026-10-01T09:17:19Z fulldoi: https://doi.org/10.1088/1367-2630/ae8b16 has_accepted_license: '1' intvolume: ' 28' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 3b79db15-b029-11f1-a721-dbd41d892ec2 grant_number: COE01 name: Quantum Science Austria (Hosten) publication: New Journal of Physics publication_identifier: eissn: - 1367-2630 publication_status: published publisher: IOP Publishing quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Cascaded optomechanical sensing for small signals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22959' abstract: - lang: eng text: 'With this status report, we aim to provide a timely snapshot of the protein engineering field as a broad and rapidly advancing discipline that integrates computational, molecular biology, structure-guided, evolutionary, and synthetic approaches to create new and improved proteins with tailored structures and useful functions. The report is organized into eight thematic areas spanning core methodologies and major application domains, including enzymes, therapeutics, detection, synthetic biology, and materials. Contributions from experts across these areas highlight both the historical foundations and recent advances in their respective fields, with particular emphasis on the growing influence of machine learning and artificial intelligence-based methods. Emerging from this broad overview is a central message: protein engineering appears to be entering a golden age, defined by a rapidly accelerating pace of progress, even as significant challenges in design, screening, and real-world application remain. Looking ahead, the continued integration of computational and experimental strategies is poised to further accelerate the impact of protein engineering across an expanding range of economically and societally important sectors, from therapeutics and molecular imaging to diagnostics, plastic recycling, and industrial chemistry.' acknowledgement: "Research in the lab of H.A. is supported by the National Institutes of Health (R01EB033172, R01EB035430, and R01AG077773).\r\n\r\nResearch in the lab of F.H.A. is supported by the US Army Research Office cooperative agreement for the Institute for Collaborative Biotechnologies (W911NF-19-2-0026) and the US Department of Energy, Office of Science, Office of Basic Energy Sciences (DE-SC0021141). This report was prepared as an account of work sponsored by an agency of the US Government. Neither the US Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the US Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof.\r\n\r\nResearch in the lab of D.B. has been supported by National Institutes of Health (NIH) (R35-GM158123-01 and R01-GM068462).\r\n\r\nResearch in the lab of H.B. is supported by grants from the Bill & Melinda Gates Foundation and Oxford Nanopore Technologies.\r\n\r\nResearch in the lab of R.E.C. is supported by grants from the Japan Society for the Promotion of Science (JSPS) (23K26794, 24H00489, and 24H02267), Japan Science and Technology Agency (JST) (JPMJCR25T3), the Mitsubishi Foundation, and the NIH (U01NS123658).\r\n\r\nResearch in the lab of P.C. is supported by grants from the Vidyasirimedhi Institute of Science and Technology (VISTEC), NSRF via the Program Management Unit for Human Resources & Institutional Development (PMU-B) Research and Innovation grant number B05F640089, and KasikornBank Public Company Limited.\r\n\r\nResearch in the lab of R.A.C. is supported by grants from the Natural Sciences and Engineering Research Council of Canada (RGPIN-2021-03484, RGPAS-2021-00017, and ALLRP-597074-24), the Human Frontier Science Program (RGP0004/2022) and the Canada Foundation for Innovation (26503 and 42695). B.J.S. was supported by an NSERC Canada Graduate Research Scholarship.\r\n\r\nResearch in the lab of V.G.H.E. is supported by grants from the European Research Council, ERC (grant number 856446, CUBE), the Novo Nordisk Foundation (Emerging Investigator grant to A.V.; grant number 0061165) and the Research Council of Norway (grant numbers 309558, Centre for Industrial Biotechnology, SFI-IB, and 257622, Bio4Fuels).\r\n\r\nThis project in the lab of R.F. was supported by Robert A. Welch Foundation (AT-0051-20221212), and the Cancer Prevention and Research Institute of Texas (grant RR230018).\r\n\r\nResearch in the lab of M.S.F. is supported by ETH Zurich and the Swiss National Science Foundation (SNSF) under grant number CR00I5-235927.\r\n\r\nThis project in the lab of J.J.G is supported by the NIH (R35 GM141881) and a National Science Foundation (NSF) Graduate Research Fellowship Program to M.C.\r\n\r\nRelated research in the lab of B.H. is supported by the German Research Foundation (DFG) Project Number 391977956—SFB 1357 Microplastics, subproject C03 and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 951375 (ERC Synergy—ArtMotor).\r\n\r\nRelated work in the lab of S.C.L.K. is supported by the NSF under Grant No. 2414074. S.C.L.K. is the Georgia Research Alliance—Vasser Wooley Chair of Molecular Design at Georgia Tech.\r\n\r\nResearch in the lab of N.K. is supported by grants from the JSPS (24H02261).\r\n\r\nThis project in the lab of B.K. was supported by the NIH (R35 GM131923).\r\n\r\nResearch in the lab of R.E.K. on bispecific antibodies is supported by a grant from the Baden-Württemberg Stiftung and various industry collaborations. Past research was funded by the Deutsche Krebshilfe, the BMBF, and the Deutsche Forschungsgemeinschaft.\r\n\r\nResearch in the lab of R.D.L. (Protein Engineering and Structural Genomics group) is supported by grants from Brazilian National Research Council—CNPq (303833/2022-0, 307370/2025-9), the Oswaldo Cruz Fondation—Fiocruz (VPPIS-004-FIO-22, IAM-005-FIO-22, VPPCB-002-FIO25), and the Brazilian National Supercomputing Center—LNCC.\r\n\r\nChemical protein synthesis research in the lab of L.L. is supported by NSFC (22137005, 22227810, T2488301) and New Cornerstone Science Foundation.\r\n\r\nResearch in the lab of M.M.M. is supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (202250/Z/16/Z); the Biotechnology and Biological Sciences Research Council (BB/W015730/1) and a UKRI Postdoc Guarantee Fellowship (Horizon Europe Guarantee via EPSRC EP/Z000823/1 to L.F.G).\r\n\r\nResearch in the lab of F.Z. is partially supported by the Natural Science Foundation of Shaanxi Province (2025SF-YBXM-421).\r\n\r\nResearch in the lab of J.K.N. is supported by the NIH (R35GM155044), Biohub, San Francisco, the Pew Charitable Trusts, The Vallee Foundation, The Shurl and Kay Curci Foundation, the Bakar Fellows Program, and a Sloan Research Fellowship. I.J.O. acknowledges support from a Gilliam Fellowship from the Howard Hughes Medical Institute.\r\n\r\nResearch in the lab of J.N.P. is supported by the Natural Science and Engineering Research Council of Canada (RGPIN-N-2018-04686) and the Canada Research Chair in Engineering of Applied Proteins (CRC-2020-00171). D.J.F. is supported by a fellowship from the Fonds de recherche du Québec.\r\n\r\nResearch in the lab of A.P. has been supported predominantly by grants from the SNSF, the European Union, the European Research Council, as well as by pre- and postdoctoral fellowships to the co-workers.\r\n\r\nResearch in the lab of Y.Q. is supported by a Horizon Europe Guarantee ERC Starting Grant (EP/Z000351/1) and a Biotechnology and Biological Sciences Research Council Research Grant (BB/W00349X/1).\r\n\r\nJ.C.R. acknowledges partial support from the SNSF Postdoc.Mobility (P500PN_214290). The author thanks Chenghao Liu and Jason Yang for fruitful discussions.\r\n\r\nResearch in the lab of S.S. is supported by a NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO, VI.Vidi.213.025) and the European Research Council, ERC (grant agreement number 101075934, ReCNNSTRCT).\r\n\r\nResearch in the lab of J.B.S. is supported by a Helmsley Charitable Trust grant and a Swim Across America grant.\r\n\r\nThis project in the lab of C.L.T. was supported by a grant from the National Institute of General Medical Sciences of the NIH (R35GM136367).\r\n\r\nResearch on ncAAs in the lab of J.A.V. is supported by a grant from the National Institute of General Medical Sciences of the NIH (R35GM133471) and a grant from the NSF (2339201). The content is solely the responsibility of the author and does not necessarily represent the official views of the NIH or the NSF.\r\n\r\nResearch in the lab of A.M.W is supported by an NIH Director’s New Innovator Award (DP2GM149548), a David and Lucille Packard Fellowship for Science and Engineering (2021-73007), an Ono Pharma Foundation Breakthrough Science Initiative Award (149802896), and the University of Wisconsin—Madison Department of Biochemistry.\r\n\r\nProjects in the lab of A.H-W.Y. are supported by NIH/NIBIB R00EB031913, UCSC startup/Innovation Catalyst Grant, and Chan Zuckerberg Initiative (2024-337820).\r\n\r\nResearch in the lab of J.Zhang is supported by NIH grants R35 CA197622, R01 DK073368, R01 DE030497, R01 HL162302, R01 CA262815, and RF1 MH126707.\r\n\r\nResearch in the lab of H. Z. is supported by the DOE Center for Advanced Bioenergy and Bioproducts Innovation (U.S. Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number DE-SC0018420), National Science Foundation (NSF) (DBI-2400058, OISE-2435374, IIS-2435755, and CHE-2505932), and National Institutes of Health (NIH) (AI144967). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the DOE, NSF or NIH.\r\n\r\nThe authors are grateful to the anonymous peer reviewers and to Anna Devor for inspiration and guidance for preparing this manuscript." article_number: gzag020 article_processing_charge: No article_type: review author: - first_name: Hui-wang full_name: Ai, Hui-wang last_name: Ai - first_name: Frances H full_name: Arnold, Frances H last_name: Arnold - first_name: Doug full_name: Barrick, Doug last_name: Barrick - first_name: Hagan full_name: Bayley, Hagan last_name: Bayley - first_name: Alfie-Louise R full_name: Brownless, Alfie-Louise R last_name: Brownless - first_name: Robert E full_name: Campbell, Robert E last_name: Campbell - first_name: Roger full_name: Castells-Graells, Roger last_name: Castells-Graells - first_name: Pimchai full_name: Chaiyen, Pimchai last_name: Chaiyen - first_name: Roberto A full_name: Chica, Roberto A last_name: Chica - first_name: Lauren O full_name: Chisholm, Lauren O last_name: Chisholm - first_name: Daniel full_name: Christ, Daniel last_name: Christ - first_name: Guo-Chao full_name: Chu, Guo-Chao last_name: Chu - first_name: Michael full_name: Chungyoun, Michael last_name: Chungyoun - first_name: Vincent G H full_name: Eijsink, Vincent G H last_name: Eijsink - first_name: Michael B full_name: Elowitz, Michael B last_name: Elowitz - first_name: Douglas J full_name: Fansher, Douglas J last_name: Fansher - first_name: Rudi full_name: Fasan, Rudi last_name: Fasan - first_name: Gabriel full_name: Foley, Gabriel last_name: Foley - first_name: Michelle S full_name: Frei, Michelle S last_name: Frei - first_name: Andreas full_name: Gagsteiger, Andreas last_name: Gagsteiger - first_name: Ruiyan full_name: Gao, Ruiyan last_name: Gao - first_name: Elizabeth M J full_name: Gillam, Elizabeth M J last_name: Gillam - first_name: Jeffrey J full_name: Gray, Jeffrey J last_name: Gray - first_name: Luis F full_name: Guerra, Luis F last_name: Guerra - first_name: Birte full_name: Höcker, Birte last_name: Höcker - first_name: Zhiyang full_name: Jin, Zhiyang last_name: Jin - first_name: Shina Caroline Lynn full_name: Kamerlin, Shina Caroline Lynn last_name: Kamerlin - first_name: Nobuyasu full_name: Koga, Nobuyasu last_name: Koga - first_name: Roland E full_name: Kontermann, Roland E last_name: Kontermann - first_name: Brian full_name: Kuhlman, Brian last_name: Kuhlman - first_name: Olivia A full_name: Langlois, Olivia A last_name: Langlois - first_name: Dongyang full_name: Li, Dongyang last_name: Li - first_name: Roberto D full_name: Lins, Roberto D last_name: Lins - first_name: Chang C full_name: Liu, Chang C last_name: Liu - first_name: Lei full_name: Liu, Lei last_name: Liu - first_name: Diego full_name: López Barreiro, Diego last_name: López Barreiro - first_name: Peilong full_name: Lu, Peilong last_name: Lu - first_name: Sohum full_name: Mehta, Sohum last_name: Mehta - first_name: Ikumi full_name: Miyazaki, Ikumi last_name: Miyazaki - first_name: Manuel M full_name: Müller, Manuel M last_name: Müller - first_name: Serge full_name: Muyldermans, Serge last_name: Muyldermans - first_name: Naoto full_name: Nemoto, Naoto last_name: Nemoto - first_name: Jeff full_name: Nivala, Jeff last_name: Nivala - first_name: James K full_name: Nuñez, James K last_name: Nuñez - first_name: Izaiah J full_name: Ornelas, Izaiah J last_name: Ornelas - first_name: Joelle N full_name: Pelletier, Joelle N last_name: Pelletier - first_name: Andreas full_name: Plückthun, Andreas last_name: Plückthun - first_name: Owen T full_name: Porth, Owen T last_name: Porth - first_name: Kridsadakorn full_name: Prakinee, Kridsadakorn last_name: Prakinee - first_name: Yujia full_name: Qing, Yujia last_name: Qing - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Sandy full_name: Schmidt, Sandy last_name: Schmidt - first_name: Oliver full_name: Seifert, Oliver last_name: Seifert - first_name: Mikhail G full_name: Shapiro, Mikhail G last_name: Shapiro - first_name: Rachna full_name: Sharma, Rachna last_name: Sharma - first_name: Nilmani full_name: Singh, Nilmani last_name: Singh - first_name: Benjamin J full_name: Smith, Benjamin J last_name: Smith - first_name: Jamie B full_name: Spangler, Jamie B last_name: Spangler - first_name: Rie full_name: Tatsumi-Koga, Rie last_name: Tatsumi-Koga - first_name: Takuya full_name: Terai, Takuya last_name: Terai - first_name: Henrik full_name: Terholsen, Henrik last_name: Terholsen - first_name: Mattias full_name: Tolhurst, Mattias last_name: Tolhurst - first_name: Katherine W full_name: Tripp, Katherine W last_name: Tripp - first_name: Vanessa Tanja full_name: Trossmann, Vanessa Tanja last_name: Trossmann - first_name: Chandra L full_name: Tucker, Chandra L last_name: Tucker - first_name: Onur full_name: Turak, Onur last_name: Turak - first_name: James A full_name: Van Deventer, James A last_name: Van Deventer - first_name: Anikó full_name: Várnai, Anikó last_name: Várnai - first_name: Isabelle F T full_name: Viana, Isabelle F T last_name: Viana - first_name: Amy M full_name: Weeks, Amy M last_name: Weeks - first_name: K Dane full_name: Wittrup, K Dane last_name: Wittrup - first_name: Kingsley L-J full_name: Wong, Kingsley L-J last_name: Wong - first_name: Chenggang full_name: Xi, Chenggang last_name: Xi - first_name: Todd O full_name: Yeates, Todd O last_name: Yeates - first_name: Andy Hsien-Wei full_name: Yeh, Andy Hsien-Wei last_name: Yeh - first_name: Jin full_name: Zhang, Jin last_name: Zhang - first_name: Tiger S full_name: Zhang, Tiger S last_name: Zhang - first_name: Huimin full_name: Zhao, Huimin last_name: Zhao - first_name: Fang full_name: Zheng, Fang last_name: Zheng - first_name: Jingyi full_name: Zhu, Jingyi last_name: Zhu - first_name: Sacha full_name: Zinn, Sacha last_name: Zinn citation: ama: 'Ai H, Arnold FH, Barrick D, et al. Protein engineering: Status report. Protein Engineering, Design and Selection. 2026;39. doi:10.1093/protein/gzag020' apa: 'Ai, H., Arnold, F. H., Barrick, D., Bayley, H., Brownless, A.-L. R., Campbell, R. E., … Zinn, S. (2026). Protein engineering: Status report. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzag020' chicago: 'Ai, Hui-wang, Frances H Arnold, Doug Barrick, Hagan Bayley, Alfie-Louise R Brownless, Robert E Campbell, Roger Castells-Graells, et al. “Protein Engineering: Status Report.” Protein Engineering, Design and Selection. Oxford University Press, 2026. https://doi.org/10.1093/protein/gzag020.' ieee: 'H. Ai et al., “Protein engineering: Status report,” Protein Engineering, Design and Selection, vol. 39. Oxford University Press, 2026.' ista: 'Ai H, Arnold FH, Barrick D, Bayley H, Brownless A-LR, Campbell RE, Castells-Graells R, Chaiyen P, Chica RA, Chisholm LO, Christ D, Chu G-C, Chungyoun M, Eijsink VGH, Elowitz MB, Fansher DJ, Fasan R, Foley G, Frei MS, Gagsteiger A, Gao R, Gillam EMJ, Gray JJ, Guerra LF, Höcker B, Jin Z, Kamerlin SCL, Koga N, Kontermann RE, Kuhlman B, Langlois OA, Li D, Lins RD, Liu CC, Liu L, López Barreiro D, Lu P, Mehta S, Miyazaki I, Müller MM, Muyldermans S, Nemoto N, Nivala J, Nuñez JK, Ornelas IJ, Pelletier JN, Plückthun A, Porth OT, Prakinee K, Qing Y, Reisenbauer J, Schmidt S, Seifert O, Shapiro MG, Sharma R, Singh N, Smith BJ, Spangler JB, Tatsumi-Koga R, Terai T, Terholsen H, Tolhurst M, Tripp KW, Trossmann VT, Tucker CL, Turak O, Van Deventer JA, Várnai A, Viana IFT, Weeks AM, Wittrup KD, Wong KL-J, Xi C, Yeates TO, Yeh AH-W, Zhang J, Zhang TS, Zhao H, Zheng F, Zhu J, Zinn S. 2026. Protein engineering: Status report. Protein Engineering, Design and Selection. 39, gzag020.' mla: 'Ai, Hui-wang, et al. “Protein Engineering: Status Report.” Protein Engineering, Design and Selection, vol. 39, gzag020, Oxford University Press, 2026, doi:10.1093/protein/gzag020.' short: H. Ai, F.H. Arnold, D. Barrick, H. Bayley, A.-L.R. Brownless, R.E. Campbell, R. Castells-Graells, P. Chaiyen, R.A. Chica, L.O. Chisholm, D. Christ, G.-C. Chu, M. Chungyoun, V.G.H. Eijsink, M.B. Elowitz, D.J. Fansher, R. Fasan, G. Foley, M.S. Frei, A. Gagsteiger, R. Gao, E.M.J. Gillam, J.J. Gray, L.F. Guerra, B. Höcker, Z. Jin, S.C.L. Kamerlin, N. Koga, R.E. Kontermann, B. Kuhlman, O.A. Langlois, D. Li, R.D. Lins, C.C. Liu, L. Liu, D. López Barreiro, P. Lu, S. Mehta, I. Miyazaki, M.M. Müller, S. Muyldermans, N. Nemoto, J. Nivala, J.K. Nuñez, I.J. Ornelas, J.N. Pelletier, A. Plückthun, O.T. Porth, K. Prakinee, Y. Qing, J. Reisenbauer, S. Schmidt, O. Seifert, M.G. Shapiro, R. Sharma, N. Singh, B.J. Smith, J.B. Spangler, R. Tatsumi-Koga, T. Terai, H. Terholsen, M. Tolhurst, K.W. Tripp, V.T. Trossmann, C.L. Tucker, O. Turak, J.A. Van Deventer, A. Várnai, I.F.T. Viana, A.M. Weeks, K.D. Wittrup, K.L.-J. Wong, C. Xi, T.O. Yeates, A.H.-W. Yeh, J. Zhang, T.S. Zhang, H. Zhao, F. Zheng, J. Zhu, S. Zinn, Protein Engineering, Design and Selection 39 (2026). das_tickbox: '1' dataavailabilitystatement: No new data were generated or analysed in support of this research. date_created: 2026-09-17T11:06:36Z date_published: 2026-07-17T00:00:00Z date_updated: 2026-10-01T09:29:15Z day: '17' ddc: - '570' department: - _id: JuRe doi: 10.1093/protein/gzag020 external_id: pmid: - '42466865' file: - access_level: open_access checksum: 4015ecfe11b3b0cac757d5bdd10d3c1d content_type: application/pdf creator: dernst date_created: 2026-10-01T09:24:22Z date_updated: 2026-10-01T09:24:22Z file_id: '23019' file_name: 2026_ProteinEngineeringDesignSelection_Ai.pdf file_size: 12603911 relation: main_file success: 1 file_date_updated: 2026-10-01T09:24:22Z fulldoi: https://doi.org/10.1093/protein/gzag020 has_accepted_license: '1' intvolume: ' 39' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Protein Engineering, Design and Selection publication_identifier: eissn: - 1741-0134 issn: - 1741-0126 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Protein engineering: Status report' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2026' ... --- OA_place: publisher _id: '21198' abstract: - lang: eng text: "In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott citation: ama: Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:10.15479/AT-ISTA-21198 apa: Scott, J. A. (2026). Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21198 chicago: Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21198. ieee: J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026. ista: Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. mla: Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21198. short: J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-02-09T14:59:53Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-10-01T09:29:03Z day: '09' ddc: - '005' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT-ISTA-21198 doi_confirm: '1' file: - access_level: closed checksum: 121c1d968bd86f3630aa7e81d5bbbcb0 content_type: application/zip creator: jscott date_created: 2026-02-17T11:46:22Z date_updated: 2026-02-17T11:46:22Z file_id: '21298' file_name: 2026_Scott_Jonathan_Thesis_Source.zip file_size: 272379252 relation: source_file - access_level: open_access checksum: 6e3e08ba474bbee8511cc8a839ab2077 content_type: application/pdf creator: jscott date_created: 2026-02-27T10:25:41Z date_updated: 2026-02-27T10:25:41Z file_id: '21366' file_name: 2026_Jonathan_Scott_Thesis.pdf file_size: 15220298 relation: main_file success: 1 file_date_updated: 2026-02-27T10:25:41Z fulldoi: https://doi.org/10.15479/AT-ISTA-21198 has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '158' project: - _id: d8f03aaa-b035-11f1-8588-d5147fa879e0 grant_number: COE12 name: Bilateral Artificial Intelligence (Lampert) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21207' relation: part_of_dissertation status: public - id: '20819' relation: part_of_dissertation status: public - id: '17411' relation: part_of_dissertation status: public - id: '18120' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Data heterogeneity and personalization in federated learning type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher _id: '21854' abstract: - lang: eng text: "As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.\r\n\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: "The research in this Ph.D. was funded in whole\r\nor in part by the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational Optimization). For open access purposes the author has applied a CC BY\r\npublic copyright license to any author accepted manuscript version arising from this submission\r\nwherever possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative assistant,\r\nChristine Francois, who always deals with our nonsense with common sense and a smile.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 citation: ama: Iofinova EB. On the utility and effects of efficiency in artificial neural networks. 2026. doi:10.15479/AT-ISTA-21854 apa: Iofinova, E. B. (2026). On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21854 chicago: Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial Neural Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21854. ieee: E. B. Iofinova, “On the utility and effects of efficiency in artificial neural networks,” Institute of Science and Technology Austria, 2026. ista: Iofinova EB. 2026. On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria. mla: Iofinova, Eugenia B. On the Utility and Effects of Efficiency in Artificial Neural Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21854. short: E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural Networks, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '1' date_created: 2026-05-11T08:43:22Z date_published: 2026-05-11T00:00:00Z date_updated: 2026-10-01T09:32:47Z day: '11' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/AT-ISTA-21854 doi_confirm: '1' file: - access_level: closed checksum: 2e148dad920e3f9b7c32796e0ba2e5f7 content_type: application/zip creator: eiofinov date_created: 2026-05-11T08:36:01Z date_updated: 2026-05-11T08:36:01Z file_id: '21856' file_name: EIofinova_thesis_FinalVersion.zip file_size: 28479571 relation: source_file - access_level: open_access checksum: b10c2933f386f532b2dbf28b19c5525c content_type: application/pdf creator: eiofinov date_created: 2026-05-13T13:10:48Z date_updated: 2026-05-13T13:10:48Z file_id: '21877' file_name: 2026_Iofinova_Eugenia_Thesis.pdf file_size: 18137757 relation: main_file success: 1 file_date_updated: 2026-05-13T13:10:48Z fulldoi: https://doi.org/10.15479/AT-ISTA-21854 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '237' project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of ISTA's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation. related_material: record: - id: '14771' relation: part_of_dissertation status: public - id: '21858' relation: part_of_dissertation status: public - id: '21859' relation: part_of_dissertation status: public - id: '21857' relation: part_of_dissertation status: public - id: '18121' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: On the utility and effects of efficiency in artificial neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22960' abstract: - lang: eng text: "We construct and characterize a sample of 146 little red dots (LRDs) across 2.0Monthly Notices of the Royal Astronomical Society. 2026;551(3). doi:10.1093/mnras/stag1567' apa: 'de Graaff, A., Hviding, R. E., Naidu, R. P., Greene, J. E., Miller, T. B., Leja, J., … van der Wel, A. (2026). Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stag1567' chicago: 'de Graaff, Anna, Raphael E Hviding, Rohan P Naidu, Jenny E Greene, Tim B Miller, Joel Leja, Jorryt J Matthee, et al. “Little Red Dots Host Black Hole Stars: A Unified Family of Gas-Reddened AGN Revealed by JWST/NIRSpec Spectroscopy.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2026. https://doi.org/10.1093/mnras/stag1567.' ieee: 'A. de Graaff et al., “Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy,” Monthly Notices of the Royal Astronomical Society, vol. 551, no. 3. Oxford University Press, 2026.' ista: 'de Graaff A, Hviding RE, Naidu RP, Greene JE, Miller TB, Leja J, Matthee JJ, Brammer G, Katz H, Bezanson R, Boogaard LA, Bose S, Chisholm J, Cleri NJ, Dayal P, Feldmann R, Fudamoto Y, Fujimoto S, Furtak LJ, Glazebrook K, Gottumukkala R, Heintz KE, Kokorev V, Labbe I, Maseda MV, McConachie I, Nanayakkara T, Nelson E, Nowaczyk P, Oesch PA, Rix H-W, Setton DJ, Torralba Torregrosa A, Walter F, Wang B, Weibel A, van der Wel A. 2026. Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy. Monthly Notices of the Royal Astronomical Society. 551(3), stag1567.' mla: 'de Graaff, Anna, et al. “Little Red Dots Host Black Hole Stars: A Unified Family of Gas-Reddened AGN Revealed by JWST/NIRSpec Spectroscopy.” Monthly Notices of the Royal Astronomical Society, vol. 551, no. 3, stag1567, Oxford University Press, 2026, doi:10.1093/mnras/stag1567.' short: A. de Graaff, R.E. Hviding, R.P. Naidu, J.E. Greene, T.B. Miller, J. Leja, J.J. Matthee, G. Brammer, H. Katz, R. Bezanson, L.A. Boogaard, S. Bose, J. Chisholm, N.J. Cleri, P. Dayal, R. Feldmann, Y. Fudamoto, S. Fujimoto, L.J. Furtak, K. Glazebrook, R. Gottumukkala, K.E. Heintz, V. Kokorev, I. Labbe, M.V. Maseda, I. McConachie, T. Nanayakkara, E. Nelson, P. Nowaczyk, P.A. Oesch, H.-W. Rix, D.J. Setton, A. Torralba Torregrosa, F. Walter, B. Wang, A. Weibel, A. van der Wel, Monthly Notices of the Royal Astronomical Society 551 (2026). das_tickbox: '1' dataavailabilitystatement: "All data used in this work are publicly available through the\r\nDAWN JWST Archive (https://dawn-cph.github.io/dja/index.h\r\ntml). The spectra used in this work are part of version 4.5 of the\r\nDJA (G. Brammer & F. Valentino 2025). We also release our complete LRD catalogue, together with all key measurements made All data used in this work are publicly available through the\r\nDAWN JWST Archive (https://dawn-cph.github.io/dja/index.h\r\ntml). The spectra used in this work are part of version 4.5 of the\r\nDJA (G. Brammer & F. Valentino 2025). We also release our complete LRD catalogue, together with all key measurements made in the modified blackbody fitting and emission-line fitting. The\r\ntable can be found at https://doi.org/10.5281/zenodo.21977747,\r\nand its contents are described in Appendix B.\r\n\r\n" date_created: 2026-09-17T11:06:40Z date_published: 2026-09-01T00:00:00Z date_updated: 2026-10-01T11:31:16Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1093/mnras/stag1567 external_id: arxiv: - '2511.21820' file: - access_level: open_access checksum: a82b93954671a12bb60d8d7a4a4d526b content_type: application/pdf creator: dernst date_created: 2026-10-01T11:25:20Z date_updated: 2026-10-01T11:25:20Z file_id: '23026' file_name: 2026_MonthNoticesRAS_deGraaff.pdf file_size: 14983705 relation: main_file success: 1 file_date_updated: 2026-10-01T11:25:20Z fulldoi: https://doi.org/10.1093/mnras/stag1567 has_accepted_license: '1' intvolume: ' 551' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: 'Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 551 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21982' abstract: - lang: eng text: A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces. acknowledged_ssus: - _id: M-Shop - _id: ScienComp acknowledgement: This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing Facility. J.B. acknowledges funding from the European Union's Horizon research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101106500. article_number: L053502 article_processing_charge: Yes (via OA deal) article_type: letter_note arxiv: 1 author: - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Jack full_name: Binysh, Jack last_name: Binysh - first_name: Anton full_name: Souslov, Anton last_name: Souslov - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 2026;113(5). doi:10.1103/m7gr-2t6j apa: Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., & Waitukaitis, S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. American Physical Society. https://doi.org/10.1103/m7gr-2t6j chicago: Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” Physical Review E. American Physical Society, 2026. https://doi.org/10.1103/m7gr-2t6j. ieee: V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis, “Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” Physical Review E, vol. 113, no. 5. American Physical Society, 2026. ista: Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5), L053502. mla: Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” Physical Review E, vol. 113, no. 5, L053502, American Physical Society, 2026, doi:10.1103/m7gr-2t6j. short: V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical Review E 113 (2026). corr_author: '1' date_created: 2026-06-10T07:36:41Z date_published: 2026-05-14T00:00:00Z date_updated: 2026-10-02T08:44:47Z day: '14' ddc: - '530' department: - _id: ScWa - _id: GradSch doi: 10.1103/m7gr-2t6j external_id: arxiv: - '2507.04982' file: - access_level: open_access checksum: 902cc8d177c8d3ae9cfe07c30375c9a9 content_type: application/pdf creator: dernst date_created: 2026-06-16T11:21:53Z date_updated: 2026-06-16T11:21:53Z file_id: '22014' file_name: 2026_PhysicalReviewE_DiazMelian.pdf file_size: 3173197 relation: main_file success: 1 file_date_updated: 2026-06-16T11:21:53Z fulldoi: https://doi.org/10.1103/m7gr-2t6j has_accepted_license: '1' intvolume: ' 113' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '23005' relation: dissertation_contains status: public scopus_import: '1' status: public title: Geometry of the vapor layer under a Leidenfrost hydrogel sphere tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2026' ... --- OA_place: publisher _id: '23005' abstract: - lang: eng text: When a Leidenfrost droplet floats on its own vapor layer, the interplay between vapor pressure, surface tension, and gravity determines its shape, and in the stable regime the underside of the droplet exhibits curvature inversion. Using interferometric imaging, we observe a different behavior for a levitated hydrogel sphere. Curvature inversion appears briefly after deposition, but the continuous vaporization process removes this feature, leading first to an oscillatory regime and eventually to a steady state without curvature inversion. We demonstrate the essential role of vaporization in shaping the hydrogel underbelly, where direct mass loss has a stronger influence than the balance between vapor pressure and elastic forces. acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian citation: ama: Diaz Melian VL. The morphology underneath a levitated hydrogel sphere. 2026. doi:10.15479/AT-ISTA-23005 apa: Diaz Melian, V. L. (2026). The morphology underneath a levitated hydrogel sphere. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-23005 chicago: Diaz Melian, Vicente L. “The Morphology underneath a Levitated Hydrogel Sphere.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-23005. ieee: V. L. Diaz Melian, “The morphology underneath a levitated hydrogel sphere,” Institute of Science and Technology Austria, 2026. ista: Diaz Melian VL. 2026. The morphology underneath a levitated hydrogel sphere. Institute of Science and Technology Austria. mla: Diaz Melian, Vicente L. The Morphology underneath a Levitated Hydrogel Sphere. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-23005. short: V.L. Diaz Melian, The Morphology underneath a Levitated Hydrogel Sphere, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-09-28T17:40:23Z date_published: 2026-09-29T00:00:00Z date_updated: 2026-10-02T08:44:47Z day: '29' ddc: - '530' - '530' - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-23005 doi_confirm: '1' file: - access_level: open_access checksum: f339bdee0a6925573687de928ca525dc content_type: application/pdf creator: vdiazmel date_created: 2026-09-29T09:22:27Z date_updated: 2026-09-29T09:56:46Z file_id: '23007' file_name: 2026_diaz-melian_vicente_Thesis.pdf file_size: 8463804 relation: main_file - access_level: closed checksum: 5b17122895fc419bfb620e23bfe7780a content_type: application/zip creator: vdiazmel date_created: 2026-09-29T09:49:32Z date_updated: 2026-09-29T09:56:46Z file_id: '23008' file_name: 2026_diaz-melian_vicente_Thesis.zip file_size: 4028974886 relation: source_file file_date_updated: 2026-09-29T09:56:46Z fulldoi: https://doi.org/10.15479/AT-ISTA-23005 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '114' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14514' relation: part_of_dissertation status: public - id: '21982' relation: part_of_dissertation status: public researchdata_availability: yes status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 supplementarymaterial: yes title: The morphology underneath a levitated hydrogel sphere tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22981' acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "I want to acknowledge the Austrian Academy of Sciences for funding through the DOC \r\nFellowship program (fellowship number 26422) and for the honest and inspirational talk by \r\nAnton Zeilinger at the award ceremony about the PhD journey. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nathalie full_name: Gruber, Nathalie id: 2C9C8316-AA17-11E9-B5C2-8BC2E5697425 last_name: Gruber citation: ama: Gruber N. Genetic strategies enabling bacterial adaptation to selective pressures. 2026. doi:10.15479/AT-ISTA-22981 apa: Gruber, N. (2026). Genetic strategies enabling bacterial adaptation to selective pressures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22981 chicago: Gruber, Nathalie. “Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22981. ieee: N. Gruber, “Genetic strategies enabling bacterial adaptation to selective pressures,” Institute of Science and Technology Austria, 2026. ista: Gruber N. 2026. Genetic strategies enabling bacterial adaptation to selective pressures. Institute of Science and Technology Austria. mla: Gruber, Nathalie. Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22981. short: N. Gruber, Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-09-23T12:25:43Z date_published: 2026-09-24T00:00:00Z date_updated: 2026-10-02T10:52:13Z day: '24' ddc: - '570' - '576' - '579' degree_awarded: PhD department: - _id: GradSch - _id: CaGu doi: 10.15479/AT-ISTA-22981 doi_confirm: '1' file: - access_level: closed checksum: 64a61a8812cefaaeffc247a409d46a23 content_type: application/pdf creator: ngruber date_created: 2026-10-01T09:00:53Z date_updated: 2026-10-01T12:34:18Z embargo: 2027-10-01 embargo_to: open_access file_id: '23020' file_name: 2026_Gruber_Nathalie_Thesis.pdf file_size: 48619027 relation: main_file - access_level: closed checksum: 942f6291750664d6d1adfb4f8b5a1735 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ngruber date_created: 2026-10-01T09:31:20Z date_updated: 2026-10-01T11:49:41Z file_id: '23021' file_name: 2026_Gruber_Nathalie_Thesis.docx file_size: 55175414 relation: source_file file_date_updated: 2026-10-01T12:34:18Z fulldoi: https://doi.org/10.15479/AT-ISTA-22981 has_accepted_license: '1' language: - iso: eng month: '09' oa_version: Published Version page: '102' project: - _id: 34cb8730-11ca-11ed-8bc3-8b3b3752a6f6 grant_number: '26422' name: Uncovering the organisational principle of bacterial genomic islands in Anti-phage defense publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Genetic strategies enabling bacterial adaptation to selective pressures type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21743' abstract: - lang: eng text: We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden–Weinstein structure. Our method integrates the Liouville 1-form of the Marsden–Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures. acknowledgement: The authors are grateful to Boris Khesin for valuable comments on the MW symplectic structure and S. Ishida thanks Albert Chern for insightful discussions on space curves and Chris Wojtan for his continuous support. M. Bauer was partially supported by NSF grant DMS-1953244 and by the Binational Science Foundation (BSF). S. Ishida was partially supported by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Some figures were generated by the software Houdini and its education license was provided by SideFX. Open access funding provided by University of Vienna. article_number: '45' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Martin full_name: Bauer, Martin last_name: Bauer - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida orcid: 0000-0002-3121-3100 - first_name: Peter W. full_name: Michor, Peter W. last_name: Michor citation: ama: Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. Journal of Nonlinear Science. 2026;36(2). doi:10.1007/s00332-026-10266-8 apa: Bauer, M., Ishida, S., & Michor, P. W. (2026). Symplectic structures on the space of space curves. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-026-10266-8 chicago: Bauer, Martin, Sadashige Ishida, and Peter W. Michor. “Symplectic Structures on the Space of Space Curves.” Journal of Nonlinear Science. Springer Nature, 2026. https://doi.org/10.1007/s00332-026-10266-8. ieee: M. Bauer, S. Ishida, and P. W. Michor, “Symplectic structures on the space of space curves,” Journal of Nonlinear Science, vol. 36, no. 2. Springer Nature, 2026. ista: Bauer M, Ishida S, Michor PW. 2026. Symplectic structures on the space of space curves. Journal of Nonlinear Science. 36(2), 45. mla: Bauer, Martin, et al. “Symplectic Structures on the Space of Space Curves.” Journal of Nonlinear Science, vol. 36, no. 2, 45, Springer Nature, 2026, doi:10.1007/s00332-026-10266-8. short: M. Bauer, S. Ishida, P.W. Michor, Journal of Nonlinear Science 36 (2026). date_created: 2026-04-16T07:29:17Z date_published: 2026-04-15T00:00:00Z date_updated: 2026-10-02T11:16:45Z day: '15' ddc: - '510' department: - _id: GradSch - _id: ChWo doi: 10.1007/s00332-026-10266-8 external_id: arxiv: - '2407.19908' file: - access_level: open_access checksum: 760de2631b6fd7d57bcd5115ed36c0a2 content_type: application/pdf creator: dernst date_created: 2026-04-28T09:55:32Z date_updated: 2026-04-28T09:55:32Z file_id: '21770' file_name: 2026_JourNonlinearScience_Bauer.pdf file_size: 1108518 relation: main_file success: 1 file_date_updated: 2026-04-28T09:55:32Z fulldoi: https://doi.org/10.1007/s00332-026-10266-8 has_accepted_license: '1' intvolume: ' 36' issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Journal of Nonlinear Science publication_identifier: eissn: - 1432-1467 issn: - 0938-8974 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '17361' relation: earlier_version status: public scopus_import: '1' status: public title: Symplectic structures on the space of space curves tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '14703' abstract: - lang: eng text: We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation. acknowledgement: 'The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospitality. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Open access funding provided by Institute of Science and Technology (IST Austria).' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida orcid: 0000-0002-3121-3100 - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: ama: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. 2026;26:349-384. doi:10.1007/s10208-024-09686-3 apa: Ishida, S., & Lavenant, H. (2026). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-024-09686-3 chicago: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” Foundations of Computational Mathematics. Springer Nature, 2026. https://doi.org/10.1007/s10208-024-09686-3. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” Foundations of Computational Mathematics, vol. 26. Springer Nature, pp. 349–384, 2026. ista: Ishida S, Lavenant H. 2026. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. 26, 349–384. mla: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” Foundations of Computational Mathematics, vol. 26, Springer Nature, 2026, pp. 349–84, doi:10.1007/s10208-024-09686-3. short: S. Ishida, H. Lavenant, Foundations of Computational Mathematics 26 (2026) 349–384. corr_author: '1' das_tickbox: '0' date_created: 2023-12-21T10:14:37Z date_published: 2026-02-01T00:00:00Z date_updated: 2026-10-02T11:17:26Z day: '01' ddc: - '000' department: - _id: GradSch - _id: ChWo doi: 10.1007/s10208-024-09686-3 external_id: arxiv: - '2312.12213' isi: - '001352503300001' file: - access_level: open_access checksum: 30671f88e792e8b75ae3e698ac4c131c content_type: application/pdf creator: dernst date_created: 2026-07-23T05:37:52Z date_updated: 2026-07-23T05:37:52Z file_id: '22384' file_name: 2026_FoundCompMath_Ishida.pdf file_size: 1240012 relation: main_file success: 1 file_date_updated: 2026-07-23T05:37:52Z fulldoi: https://doi.org/10.1007/s10208-024-09686-3 has_accepted_license: '1' intvolume: ' 26' isi: 1 keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 349-384 project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 issn: - 1615-3375 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 26 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20657' abstract: - lang: eng text: 'The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². ' acknowledgement: The first author is supported by the European Research Council (ERC), grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. I 02979-N35. The second author is supported by the European Research Council (ERC), grant “GeoScape” and by the Hungarian Science Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach citation: ama: Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. Discrete & Computational Geometry. 2026;75:597-624. doi:10.1007/s00454-025-00796-5 apa: Edelsbrunner, H., & Pach, J. (2026). Maximum Betti numbers of Čech complexes. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-025-00796-5 chicago: Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” Discrete & Computational Geometry. Springer Nature, 2026. https://doi.org/10.1007/s00454-025-00796-5. ieee: H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” Discrete & Computational Geometry, vol. 75. Springer Nature, pp. 597–624, 2026. ista: Edelsbrunner H, Pach J. 2026. Maximum Betti numbers of Čech complexes. Discrete & Computational Geometry. 75, 597–624. mla: Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” Discrete & Computational Geometry, vol. 75, Springer Nature, 2026, pp. 597–624, doi:10.1007/s00454-025-00796-5. short: H. Edelsbrunner, J. Pach, Discrete & Computational Geometry 75 (2026) 597–624. corr_author: '1' das_tickbox: '0' date_created: 2025-11-19T09:44:58Z date_published: 2026-03-01T00:00:00Z date_updated: 2026-10-02T11:48:00Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s00454-025-00796-5 ec_funded: 1 external_id: arxiv: - '2310.14801' isi: - '001610592600001' file: - access_level: open_access checksum: c17c014dbbf5be702195c737890251c8 content_type: application/pdf creator: dernst date_created: 2026-07-27T08:11:05Z date_updated: 2026-07-27T08:11:05Z file_id: '22410' file_name: 2026_DiscreteCompGeom_Edelsbrunner.pdf file_size: 546483 relation: main_file success: 1 file_date_updated: 2026-07-27T08:11:05Z fulldoi: https://doi.org/10.1007/s00454-025-00796-5 has_accepted_license: '1' intvolume: ' 75' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 597-624 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '17146' relation: earlier_version status: public researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Maximum Betti numbers of Čech complexes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2026' ... --- OA_place: repository OA_type: green _id: '20585' abstract: - lang: eng text: Motivated by applications in medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided. acknowledgement: "This project has received funding from the European Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund\r\n(FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR\r\n109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sebastiano full_name: Cultrera di Montesano, Sebastiano id: 34D2A09C-F248-11E8-B48F-1D18A9856A87 last_name: Cultrera di Montesano orcid: 0000-0001-6249-0832 - first_name: Ondrej full_name: Draganov, Ondrej id: 2B23F01E-F248-11E8-B48F-1D18A9856A87 last_name: Draganov orcid: 0000-0003-0464-3823 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Morteza full_name: Saghafian, Morteza id: f86f7148-b140-11ec-9577-95435b8df824 last_name: Saghafian citation: ama: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. Foundations of Data Science. 2026;8:30-62. doi:10.3934/fods.2025003 apa: Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (2026). Chromatic alpha complexes. Foundations of Data Science. AIMS. https://doi.org/10.3934/fods.2025003 chicago: Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” Foundations of Data Science. AIMS, 2026. https://doi.org/10.3934/fods.2025003. ieee: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” Foundations of Data Science, vol. 8. AIMS, pp. 30–62, 2026. ista: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2026. Chromatic alpha complexes. Foundations of Data Science. 8, 30–62. mla: Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” Foundations of Data Science, vol. 8, AIMS, 2026, pp. 30–62, doi:10.3934/fods.2025003. short: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, Foundations of Data Science 8 (2026) 30–62. corr_author: '1' date_created: 2025-11-02T23:01:33Z date_published: 2026-03-01T00:00:00Z date_updated: 2026-10-02T11:56:12Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.3934/fods.2025003 ec_funded: 1 external_id: arxiv: - '2212.03128' fulldoi: https://doi.org/10.3934/fods.2025003 has_accepted_license: '1' intvolume: ' 8' keyword: - Topological data analysis - Delaunay mosaic - alpha complex - chromatic sets - persistent homology - kernel/image/cokernel persistent homology - radius function - discrete Morse theory - exact sequences language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2212.03128 mathsc: - 62R40 - 55N31 - 68T09 - 57Q70 month: '03' oa: 1 oa_version: Preprint page: 30-62 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _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 publication: Foundations of Data Science publication_identifier: eissn: - 2639-8001 publication_status: published publisher: AIMS quality_controlled: '1' related_material: record: - id: '15091' relation: earlier_version status: public scopus_import: '1' status: public title: Chromatic alpha complexes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2026' ... --- OA_place: publisher _id: '22804' abstract: - lang: eng text: 'Embryo cleavage — a series of rapid, reductive cell divisions — is the first morphogenetic movement following fertilisation. It lays the foundation for subsequent developmental events, including gastrulation, germ layer specification, organogenesis, and the establishment of the overall body plan. Two major modes of cleavage exist in the animal kingdom: holoblastic (complete) and meroblastic (incomplete) cleavage. Because holoblastic cleavage resembles canonical cytokinesis, its biochemical and mechanical basis has been extensively studied — an annular contractile ring forms at the equator and constricts in a purse-string-like manner, leading to the complete separation of two daughter cells. In contrast, although meroblastic cleavage occurs widely across the animal kingdom (e.g. in fish, reptiles, birds, and cephalopod molluscs), its mechanical basis remains largely unclear. During meroblastic cleavage, the cytokinetic furrow forms only at one pole and does not traverse the entire embryo, raising the question of how cytokinesis proceeds in the absence of a closed contractile ring. Moreover, the resulting daughter cells are not fully separated from the underlying yolk compartment, and how these blastomeres are subsequently cellularised remains unknown. This thesis takes the zebrafish as a model organism to address both questions. The first part characterises the biochemical and mechanical mechanisms underlying non-canonical meroblastic cleavage, revealing a two-phase process in which actomyosin cable contraction and cadherin-mediated membrane adhesion act sequentially to drive furrow ingression and invagination. The second part sheds light on the spatiotemporal dynamics by which individual blastomeres become cellularised, and uncovers a previously unrecognised contribution of central blastomeres to the yolk syncytial layer.' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "I gratefully acknowledge the NOMIS Stiftung (Project ID 5061.844, Cytoplasmic\r\nself-organization into cell-like compartments as a common guiding principle in\r\nearly animal development) for funding my doctoral studies." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xin full_name: Tong, Xin id: 50F65CDC-AA30-11E9-A72B-8A12E6697425 last_name: Tong citation: ama: Tong X. Towards a deeper understanding of meroblastic cleavage. 2026. doi:10.15479/AT-ISTA-22804 apa: Tong, X. (2026). Towards a deeper understanding of meroblastic cleavage. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22804 chicago: Tong, Xin. “Towards a Deeper Understanding of Meroblastic Cleavage.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22804. ieee: X. Tong, “Towards a deeper understanding of meroblastic cleavage,” Institute of Science and Technology Austria, 2026. ista: Tong X. 2026. Towards a deeper understanding of meroblastic cleavage. Institute of Science and Technology Austria. mla: Tong, Xin. Towards a Deeper Understanding of Meroblastic Cleavage. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22804. short: X. Tong, Towards a Deeper Understanding of Meroblastic Cleavage, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-09-04T11:54:20Z date_published: 2026-07-12T00:00:00Z date_updated: 2026-10-05T08:56:10Z day: '12' ddc: - '596' - '532' - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/AT-ISTA-22804 doi_confirm: '1' file: - access_level: closed checksum: fdcc187a5a92e785da0eff8936fb127e content_type: application/zip creator: xtong date_created: 2026-09-11T13:04:37Z date_updated: 2026-09-14T08:28:06Z file_id: '22909' file_name: 2026_TONG_Xin_Thesis.zip file_size: 126983933 relation: source_file - access_level: open_access checksum: 23ee39b3f08bccd46acfd332e67f5232 content_type: application/pdf creator: xtong date_created: 2026-09-14T12:30:07Z date_updated: 2026-09-14T12:48:53Z file_id: '22930' file_name: 2026_TONG_Xin_Thesis.pdf file_size: 46855054 relation: main_file file_date_updated: 2026-09-14T12:48:53Z fulldoi: https://doi.org/10.15479/AT-ISTA-22804 has_accepted_license: '1' keyword: - meroblastic cleavage - cytokinesis - active gel theory - embryogenesis - zebrafish - adhesion language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '121' project: - _id: 917c023a-16d5-11f0-9cad-eb5cafc52090 name: Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development publication_identifier: isbn: - 978-3-99078-080-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '22777' relation: research_data status: public - id: '22807' relation: part_of_dissertation status: public researchdata_availability: upon request status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Towards a deeper understanding of meroblastic cleavage tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '22777' acknowledged_ssus: - _id: Bio - _id: LifeSc article_processing_charge: No author: - first_name: Xin full_name: Tong, Xin id: 50F65CDC-AA30-11E9-A72B-8A12E6697425 last_name: Tong citation: ama: Tong X. Towards a deeper understanding of meroblastic cleavage - supplementary movies. 2026. doi:10.15479/AT-ISTA-22777 apa: Tong, X. (2026). Towards a deeper understanding of meroblastic cleavage - supplementary movies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22777 chicago: Tong, Xin. “Towards a Deeper Understanding of Meroblastic Cleavage - Supplementary Movies.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22777. ieee: X. Tong, “Towards a deeper understanding of meroblastic cleavage - supplementary movies.” Institute of Science and Technology Austria, 2026. ista: Tong X. 2026. Towards a deeper understanding of meroblastic cleavage - supplementary movies, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22777. mla: Tong, Xin. Towards a Deeper Understanding of Meroblastic Cleavage - Supplementary Movies. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22777. short: X. Tong, (2026). corr_author: '1' date_created: 2026-09-03T10:48:15Z date_published: 2026-09-04T00:00:00Z date_updated: 2026-10-05T08:56:09Z day: '4' department: - _id: GradSch - _id: CaHe doi: 10.15479/AT-ISTA-22777 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: ba2d20babb1a8e437b41c513c4d226a4 content_type: text/plain creator: xtong date_created: 2026-09-03T10:47:23Z date_updated: 2026-09-03T10:47:23Z file_id: '22779' file_name: README.txt file_size: 223 relation: main_file success: 1 - access_level: open_access checksum: 59565d43eca072572e37c81d640b8450 content_type: video/avi creator: xtong date_created: 2026-09-03T10:53:55Z date_updated: 2026-09-03T10:53:55Z file_id: '22780' file_name: Movie S1_brightfield.avi file_size: 1137586 relation: main_file success: 1 - access_level: open_access checksum: 2c0740d4555b308e3248f1695042df7b content_type: video/avi creator: xtong date_created: 2026-09-03T10:58:05Z date_updated: 2026-09-03T10:58:05Z file_id: '22796' file_name: Movie S2_membrane.avi file_size: 2400912 relation: main_file success: 1 - access_level: open_access checksum: 79cd5fc64390332a64797e9b6a5cc8ba content_type: video/avi creator: xtong date_created: 2026-09-03T10:54:09Z date_updated: 2026-09-03T10:54:09Z file_id: '22781' file_name: Movie S3_furrow_geometry.avi file_size: 1881482 relation: main_file success: 1 - access_level: open_access checksum: d67a958b90555207bd7282aa3ef3b26d content_type: video/avi creator: xtong date_created: 2026-09-03T10:54:16Z date_updated: 2026-09-03T10:54:16Z file_id: '22782' file_name: Movie S4_3D_reconstruction.avi file_size: 1613954 relation: main_file success: 1 - access_level: open_access checksum: f41a1085575416d5a1d2fb2238a59c73 content_type: video/avi creator: xtong date_created: 2026-09-03T10:54:25Z date_updated: 2026-09-03T10:54:25Z file_id: '22783' file_name: Movie S5_Factin_low_mag.avi file_size: 2133352 relation: main_file success: 1 - access_level: open_access checksum: 17026cb264cb73e13d9d9ac8bea1cc8c content_type: video/avi creator: xtong date_created: 2026-09-03T10:54:59Z date_updated: 2026-09-03T10:54:59Z file_id: '22784' file_name: Movie S6_actin_in_furrow.avi file_size: 7393622 relation: main_file success: 1 - access_level: open_access checksum: 010c876444b886d1387eb6a6048e0197 content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:26Z date_updated: 2026-09-03T10:56:26Z file_id: '22785' file_name: Movie S7_Factin_myosin_high_res.avi file_size: 39303510 relation: main_file success: 1 - access_level: open_access checksum: bfafa5c1511c82c4add84de309bad1f8 content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:41Z date_updated: 2026-09-03T10:56:41Z file_id: '22786' file_name: Movie S8_wt-video_actin_flow_div_qxx_representative.avi file_size: 53493338 relation: main_file success: 1 - access_level: open_access checksum: 9dc8da0bc297f10a3c2f1483c7193ab0 content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:45Z date_updated: 2026-09-03T10:56:45Z file_id: '22787' file_name: Movie S9_double_ablation_image_qxx.avi file_size: 25447996 relation: main_file success: 1 - access_level: open_access checksum: a5092a927e0824f7b57ac38c7afce1be content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:51Z date_updated: 2026-09-03T10:56:51Z file_id: '22788' file_name: Movie S10_laser_ablations.avi file_size: 13258430 relation: main_file success: 1 - access_level: open_access checksum: 223717789c6c883b960d317da0bff8ec content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:50Z date_updated: 2026-09-03T10:56:50Z file_id: '22789' file_name: Movie S11_laser_ablation_flow_field.avi file_size: 6224716 relation: main_file success: 1 - access_level: open_access checksum: 06287e939c40d9a6deef52c01b506491 content_type: video/avi creator: xtong date_created: 2026-09-03T10:56:58Z date_updated: 2026-09-03T10:56:58Z file_id: '22790' file_name: Movie S12_long_cut.avi file_size: 11416868 relation: main_file success: 1 - access_level: open_access checksum: 6ddc1d526556e53fb2364e9c03135b6c content_type: video/avi creator: xtong date_created: 2026-09-03T10:57:20Z date_updated: 2026-09-03T10:57:20Z file_id: '22791' file_name: Movie S13_carhoa_phenotypes.avi file_size: 37334036 relation: main_file success: 1 - access_level: open_access checksum: 34410ea9d4c79c8ce3cc6272d283f384 content_type: video/avi creator: xtong date_created: 2026-09-03T10:57:17Z date_updated: 2026-09-03T10:57:17Z file_id: '22792' file_name: Movie S14_carhoa-video_actin_flow_div_qxx_representative.avi file_size: 24196604 relation: main_file success: 1 - access_level: open_access checksum: 343f8d51cd1ff3f8bbdbbc0a86e7117f content_type: video/avi creator: xtong date_created: 2026-09-03T10:57:20Z date_updated: 2026-09-03T10:57:20Z file_id: '22793' file_name: Movie S15_Cdh1_Factin.avi file_size: 3399188 relation: main_file success: 1 - access_level: open_access checksum: a48d888dc7994e54390c55deb0976f5a content_type: video/avi creator: xtong date_created: 2026-09-03T10:57:21Z date_updated: 2026-09-03T10:57:21Z file_id: '22794' file_name: Movie S16_cafree.avi file_size: 1253862 relation: main_file success: 1 - access_level: open_access checksum: ac4790a151352cc72534ec55468acebe content_type: video/avi creator: xtong date_created: 2026-09-03T10:57:22Z date_updated: 2026-09-03T10:57:22Z file_id: '22795' file_name: Movie S17_carhoa.avi file_size: 2268762 relation: main_file success: 1 file_date_updated: 2026-09-03T10:58:05Z fulldoi: https://doi.org/10.15479/AT-ISTA-22777 has_accepted_license: '1' month: '9' oa: 1 oa_version: None project: - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publisher: Institute of Science and Technology Austria related_material: record: - id: '22804' relation: used_in_publication status: public status: public title: Towards a deeper understanding of meroblastic cleavage - supplementary movies tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22964' abstract: - lang: eng text: We investigate whether the nonaccreting phases found in thin, locally isothermal circumbinary disks survive when the disk thermodynamics are evolved self-consistently. We present grid-based hydrodynamics simulations of circumbinary accretion with an energy equation that includes viscous and hydrodynamic heating coupled to radiative blackbody cooling in the high-Mach number regime. We find that, although gas accumulates and heats at the far edge of the circumbinary cavity, the regions that launch accretion streams remain comparatively cold, leading to potentially long-lived suppression of the binary accretion rate as the large-scale feeding rate is reduced towards the Eddington limit. This runaway nonaccretion problem, however, is weakened relative to locally isothermal solutions. Despite their low accretion rates, binaries interacting with disks in a nonaccreting phase can remain sufficiently luminous and variable at optical and near-infrared frequencies to be detectable in upcoming wide-field surveys such as LSST and the Roman Space Telescope. Because of the effective truncation of the surrounding disk, though, such systems are comparatively faint in high energy, photoionizing emission, and may therefore appear as intrinsically X-ray–weak active galactic nuclei with weak or absent emission line features. We additionally suggest an update to grid-based sink prescriptions for approximating mass loss across an unresolved horizon when including an energy conservation equation. acknowledgement: "This work was supported by the European Union’s Horizon 2023 research and innovation program under Marie Sklodowska-Curie grant agreement No. 101148364, and by Sapere Aude Starting grant No. 121587 through the Danish Independent Research Fund. It was additionally supported by NSF AAG No. 2511544. CT acknowledges many helpful conversations on binary accretion at the workshop Climbing Cosmic Peaks through the Sexten Center for Astrophysics Riccardo Giacconi. In particular, we thank Zoltan Haiman and Massimo Dotti for discussions on optical time-domain searches; Andrew MacFadyen, Alessia Franchini, Magdalena Siwek, and Mark Avara for conversations on binary accretion dynamics; Alessandra De Rosa for an insightful question on ionizing emission; and Jessie Runnoe for slope-side discussions on AGN broad-line regions. C.T. additionally thanks Jonathan Zrake for helpful comments on this manuscript and the anonymous reviewer for an engaging and insightful report. This work was conceived of, performed, and written by humans: C.T., D.O.N., D.J.D. Computation time was supported through the Tycho supercomputer hosted at the SCIENCE HPC center at the University of Copenhagen.\r\nSoftware: Sailfish (J. Zrake & A. MacFadyen 2024), numpy (C. R. Harris et al. 2020), scipy (P. Virtanen et al. 2020), matplotlib (J. D. Hunter 2007), cmasher (E. van der Velden 2020)." article_number: '26' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Christopher full_name: Tiede, Christopher last_name: Tiede - first_name: David W full_name: O'Neill, David W id: 3fc12674-2d69-11f1-a6bf-b826b45a1150 last_name: O'Neill - first_name: Daniel J. full_name: D’Orazio, Daniel J. last_name: D’Orazio citation: ama: Tiede C, O’Neill DW, D’Orazio DJ. Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. The Astrophysical Journal. 2026;1008(1). doi:10.3847/1538-4357/ae914e apa: Tiede, C., O’Neill, D. W., & D’Orazio, D. J. (2026). Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ae914e chicago: Tiede, Christopher, David W O’Neill, and Daniel J. D’Orazio. “Dynamics and Detectability of Long-Lived Nonaccretion Phases for Massive Black Hole Binaries in Cold Thermally Regulating Disks.” The Astrophysical Journal. IOP Publishing, 2026. https://doi.org/10.3847/1538-4357/ae914e. ieee: C. Tiede, D. W. O’Neill, and D. J. D’Orazio, “Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks,” The Astrophysical Journal, vol. 1008, no. 1. IOP Publishing, 2026. ista: Tiede C, O’Neill DW, D’Orazio DJ. 2026. Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. The Astrophysical Journal. 1008(1), 26. mla: Tiede, Christopher, et al. “Dynamics and Detectability of Long-Lived Nonaccretion Phases for Massive Black Hole Binaries in Cold Thermally Regulating Disks.” The Astrophysical Journal, vol. 1008, no. 1, 26, IOP Publishing, 2026, doi:10.3847/1538-4357/ae914e. short: C. Tiede, D.W. O’Neill, D.J. D’Orazio, The Astrophysical Journal 1008 (2026). das_tickbox: '0' date_created: 2026-09-20T22:01:48Z date_published: 2026-09-01T00:00:00Z date_updated: 2026-10-06T10:45:07Z day: '01' ddc: - '520' department: - _id: ZoHa doi: 10.3847/1538-4357/ae914e external_id: arxiv: - '2606.04082' file: - access_level: open_access checksum: f3fa2d7a10b75b74290d7a9a68a3d367 content_type: application/pdf creator: dernst date_created: 2026-10-06T10:44:15Z date_updated: 2026-10-06T10:44:15Z file_id: '23061' file_name: 2026_AstrophysicalJour_Tiede.pdf file_size: 5621643 relation: main_file success: 1 file_date_updated: 2026-10-06T10:44:15Z fulldoi: https://doi.org/10.3847/1538-4357/ae914e has_accepted_license: '1' intvolume: ' 1008' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1008 year: '2026' ... --- OA_type: closed access _id: '22965' abstract: - lang: eng text: Manganese-based aqueous zinc-ion batteries (AZIBs) have emerged as promising candidates for large-scale energy storage owing to their low cost, intrinsic safety, and the abundance of constituent elements. However, their practical deployment is still restricted by severe capacity fading caused by Jahn–Teller-induced structural instability and sluggish Zn2+ transport in the cathode. Although surface coating, heteroatom doping, and structural regulation have been widely explored to improve Mn-based cathodes, these approaches may suffer from increased interfacial resistance, compositional complexity, or limited control over the intrinsic electronic structure. In this context, oxygen-vacancy engineering offers a more direct route to modulate local coordination environments and accelerate Zn2+/H+ storage kinetics. Herein, lattice-level defect engineering of a dense Mn2O3 host is achieved through a metal–organic framework-derived synthesis followed by mild secondary annealing. The introduced oxygen vacancies regulate the local electronic structure and coordination environment, thereby facilitating Zn2+ diffusion, accelerating charge-transfer kinetics, and improving electrochemical reversibility. Combined experimental and theoretical investigations further show that oxygen-vacancy engineering enhances electronic conductivity, reduces the Zn2+ migration barrier, and enables a reversible dual-ion storage mechanism involving both H+ and Zn2+. Benefiting from these effects, the Zn‖Vo-Mn2O3 battery delivers a high specific capacity of 359 mAh g−1 at 0.3 A g−1, maintains 210 mAh g−1 at 6 A g−1, and retains 74.3% of its capacity after 10 000 cycles at 12 A g−1 after only 150 s of initial preconditioning. This work highlights oxygen-vacancy engineering as an effective route to enhancing the kinetic and structural stability of Mn-based cathodes for advanced AZIBs. acknowledgement: 'Ao Y. acknowledges financial support from the China Scholarship Council (No. 202208320041), the National Natural Science Foundation of China (No. 22475231), and the Shenzhen Science and Technology Planning Project (No. KJZD20230923115227054). The XAS experiments were performed in collaboration with ALBA staff at the NOTOS beamline of ALBA Synchrotron (experiment ID: 2024028418), Barcelona, Spain. JL is a Serra Húnter Fellow and is grateful to the Academia Excellence program (Generalitat de Catalunya) and to the project PID2024-156765OB-C21 funded by MICIU/AEI/10.13039/501100011033 and the European Regional Development Fund (FEDER), and to the María de Maeztu Units of Excellence Programme CEX2023-001300 M, funded by MCIN/AEI/10.13039/501100011033.' article_processing_charge: No article_type: original author: - first_name: Ao full_name: Yu, Ao last_name: Yu - first_name: Xingqi full_name: Chang, Xingqi last_name: Chang - first_name: Xuan full_name: Lu, Xuan last_name: Lu - first_name: Ren full_name: He, Ren id: 366c4efa-f61c-11f0-808b-d12a4547ac69 last_name: He - first_name: Linlin full_name: Yang, Linlin last_name: Yang - first_name: Jiali full_name: Chai, Jiali last_name: Chai - first_name: Xiaoyu full_name: Bi, Xiaoyu last_name: Bi - first_name: Jesús full_name: Chacón-Borrero, Jesús last_name: Chacón-Borrero - first_name: Karol V. full_name: Mejia-Centeno, Karol V. last_name: Mejia-Centeno - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Eduardo full_name: Villalobos-Portillo, Eduardo last_name: Villalobos-Portillo - first_name: Qirong full_name: Liu, Qirong last_name: Liu - first_name: Jian full_name: Shang, Jian last_name: Shang - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Yu A, Chang X, Lu X, et al. Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries. Journal of Materials Chemistry A. 2026. doi:10.1039/d6ta05844b apa: Yu, A., Chang, X., Lu, X., He, R., Yang, L., Chai, J., … Cabot, A. (2026). Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries. Journal of Materials Chemistry A. Royal Society of Chemistry. https://doi.org/10.1039/d6ta05844b chicago: Yu, Ao, Xingqi Chang, Xuan Lu, Ren He, Linlin Yang, Jiali Chai, Xiaoyu Bi, et al. “Lattice-Level Defect Engineering of Dense Mn2O3 Hosts Unlocks Fast H+/Zn2+ Storage and Long-Life Aqueous Zinc-Ion Batteries.” Journal of Materials Chemistry A. Royal Society of Chemistry, 2026. https://doi.org/10.1039/d6ta05844b. ieee: A. Yu et al., “Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries,” Journal of Materials Chemistry A. Royal Society of Chemistry, 2026. ista: Yu A, Chang X, Lu X, He R, Yang L, Chai J, Bi X, Chacón-Borrero J, Mejia-Centeno KV, Llorca J, Villalobos-Portillo E, Liu Q, Shang J, Cabot A. 2026. Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries. Journal of Materials Chemistry A. mla: Yu, Ao, et al. “Lattice-Level Defect Engineering of Dense Mn2O3 Hosts Unlocks Fast H+/Zn2+ Storage and Long-Life Aqueous Zinc-Ion Batteries.” Journal of Materials Chemistry A, Royal Society of Chemistry, 2026, doi:10.1039/d6ta05844b. short: A. Yu, X. Chang, X. Lu, R. He, L. Yang, J. Chai, X. Bi, J. Chacón-Borrero, K.V. Mejia-Centeno, J. Llorca, E. Villalobos-Portillo, Q. Liu, J. Shang, A. Cabot, Journal of Materials Chemistry A (2026). das_tickbox: '1' dataavailabilitystatement: 'The data that support the findings of this study are available within the manuscript and the corresponding supplementary information (SI). Data are available upon request from the authors. Supplementary information is available. See DOI: https://doi.org/10.1039/d6ta05844b.' date_created: 2026-09-20T22:01:48Z date_published: 2026-08-31T00:00:00Z date_updated: 2026-10-06T10:34:27Z day: '31' department: - _id: MaIb doi: 10.1039/d6ta05844b fulldoi: https://doi.org/10.1039/d6ta05844b language: - iso: eng month: '08' oa_version: None publication: Journal of Materials Chemistry A publication_identifier: eissn: - 2050-7496 issn: - 2050-7488 publication_status: epub_ahead publisher: Royal Society of Chemistry quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Lattice-level defect engineering of dense Mn2O3 hosts unlocks fast H+/Zn2+ storage and long-life aqueous zinc-ion batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22967' abstract: - lang: eng text: Alkali salts are widely used in solution processing, yet the corresponding cations are often assumed to remain in the liquid phase. Here, we show that alkali ions introduced during the solution synthesis of SnSe are retained through particle isolation and continue to influence the material during subsequent thermal processing, where they shape the evolution of the final polycrystalline material. Different SnSe powders were prepared using Li+, Na+, and K+ precursors, as well as tetramethylammonium (TMA+) precursors as a nonalkali reference for comparison, and all samples were consolidated under identical conditions. Although all three alkali ions were found in the matrix, at grain boundaries, and in segregated nanoscale regions, they partitioned differently and resulted in distinct grain sizes, defect distributions, and therefore transport properties. Li induced the strongest grain size heterogeneity and the lowest energy barriers, Na the best overall balance between carrier concentration and mobility, and K the broadest alkali-rich grain boundary regions along with the strongest interfacial penalty to charge carrier transport. These results show that residual alkali ions are not just remnants of solution synthesis but active determinants of microstructure and thermoelectric performance in SnSe. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: "ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), Juan Aguilera Servin from the Nanofabrication facility (NNF). Special acknowledgments to the Ibá\r\nez group for their fruitful discussions and insights. K.M. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413 and PETRAIII at DESY for the synchrotron X-ray measurements under proposal No. I-20241048 EC. JL is a Serra Húnter Fellow and is grateful to the Academia Excellence program (Generalitat de Catalunya), project PID2024-156765OB-C21 funded by MICIU/AEI/10.13039/501100011033 and the European Regional Development Fund (FEDER), and María de Maeztu Units of Excellence Programme CEX2023-001300 M, funded by MCIN/AEI 10.13039/501100011033. VG and SD acknowledge the use of resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411, the National Natural Science Foundation of China (NSFC) (Grants No. 22209034)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Christine full_name: Fiedler, Christine id: bd3fceba-dc74-11ea-a0a7-c17f71817366 last_name: Fiedler - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Navita full_name: Navita, Navita id: 6ebe278d-ba0b-11ee-8184-f34cdc671de4 last_name: Navita orcid: 0000-0001-7408-8197 - first_name: Krishnendu full_name: Maji, Krishnendu id: 76bc9e9f-ba0b-11ee-8184-90edabd17a58 last_name: Maji - first_name: Tobias full_name: Kleinhanns, Tobias id: 8BD9DE16-AB3C-11E9-9C8C-2A03E6697425 last_name: Kleinhanns orcid: 0000-0003-1537-7436 - first_name: Jordi full_name: Llorca, Jordi last_name: Llorca - first_name: Qi full_name: Wang, Qi id: 0d37923a-aca1-11ef-951f-fd411b71d5f0 last_name: Wang - first_name: Maria Garcia full_name: Ramon, Maria Garcia id: 1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9 last_name: Ramon - first_name: Sambit full_name: Das, Sambit last_name: Das - first_name: Vikram full_name: Gavini, Vikram last_name: Gavini - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Fiedler C, Horta S, Jakhar N, et al. Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. Chemistry of Materials. 2026;38(18):9323–9332. doi:10.1021/acs.chemmater.6c01284 apa: Fiedler, C., Horta, S., Jakhar, N., Maji, K., Kleinhanns, T., Llorca, J., … Ibáñez, M. (2026). Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.6c01284 chicago: Fiedler, Christine, Sharona Horta, Navita Jakhar, Krishnendu Maji, Tobias Kleinhanns, Jordi Llorca, Qi Wang, et al. “Alkali Ions Retained from Synthesis Govern Microstructure and Transport in Solution-Processed SnSe.” Chemistry of Materials. American Chemical Society, 2026. https://doi.org/10.1021/acs.chemmater.6c01284. ieee: C. Fiedler et al., “Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe,” Chemistry of Materials, vol. 38, no. 18. American Chemical Society, pp. 9323–9332, 2026. ista: Fiedler C, Horta S, Jakhar N, Maji K, Kleinhanns T, Llorca J, Wang Q, Ramon MG, Das S, Gavini V, Liu Y, Ibáñez M. 2026. Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe. Chemistry of Materials. 38(18), 9323–9332. mla: Fiedler, Christine, et al. “Alkali Ions Retained from Synthesis Govern Microstructure and Transport in Solution-Processed SnSe.” Chemistry of Materials, vol. 38, no. 18, American Chemical Society, 2026, pp. 9323–9332, doi:10.1021/acs.chemmater.6c01284. short: C. Fiedler, S. Horta, N. Jakhar, K. Maji, T. Kleinhanns, J. Llorca, Q. Wang, M.G. Ramon, S. Das, V. Gavini, Y. Liu, M. Ibáñez, Chemistry of Materials 38 (2026) 9323–9332. corr_author: '1' das_tickbox: '0' date_created: 2026-09-21T10:33:48Z date_published: 2026-09-22T00:00:00Z date_updated: 2026-10-06T12:16:03Z day: '22' ddc: - '540' department: - _id: MaIb - _id: GradSch - _id: NanoFab doi: 10.1021/acs.chemmater.6c01284 ec_funded: 1 external_id: pmid: - '42787739' file: - access_level: open_access checksum: 15e7866ca4fd57f5526737945651a6f2 content_type: application/pdf creator: dernst date_created: 2026-10-06T12:11:04Z date_updated: 2026-10-06T12:11:04Z file_id: '23063' file_name: 2026_ChemistryMaterials_Fiedler.pdf file_size: 7461570 relation: main_file success: 1 file_date_updated: 2026-10-06T12:11:04Z fulldoi: https://doi.org/10.1021/acs.chemmater.6c01284 has_accepted_license: '1' intvolume: ' 38' issue: '18' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 9323–9332 pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Chemistry of Materials publication_identifier: eissn: - 1520-5002 issn: - 0897-4756 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Alkali ions retained from synthesis govern microstructure and transport in solution-processed SnSe tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22972' abstract: - lang: eng text: Genomic measurements of DNA methylation, gene expression or protein levels are becoming more prevalent and are increasingly used to study health outcomes. However, most proposed association testing methods consider only marginal effects of each feature on a single outcome variable and are not set up to handle highly correlated, continuous data. Here, we introduce MAJA, a method to learn shared and outcome-specific effects for multiple traits in multi-omics data. MAJA determines the unique contribution of individual loci, genes, or molecular pathways to variation in one or more traits, conditional on all other measured “omics” data genome-wide. Simulations show MAJA accurately finds shared and distinct associations between omics-data and multiple traits and estimates omics-specific (co)variances, allowing for sparsity and correlations within the data. Applying MAJA to 12 outcome traits in Generation Scotland methylation data (n = 18 264), we find novel shared epigenetic probes among cholesterol metabolism, osteoarthritis, blood pressure and asthma. In contrast to marginal testing, we find only 10 CpG probes with significant effects above the genome-wide background. This highlights the need for joint association testing in highly correlated methylation data from whole blood and for studies of increased sample size in order to refine epigenomic associations in observational data. acknowledged_ssus: - _id: ScienComp acknowledgement: 'We thank members of the Medical Genomics group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to MRR [PCEGP3-181181], and by core funding from the Institute of Science and Technology Austria. We would like to acknowledge the participants and investigators of the Generation Scotland and Lothian Birth Cohort studies. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. Genotyping and methylation typing of the GS: SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” (STRADL) Reference 104036/Z/14/Z]. DNA methylation data for Generation Scotland was also funded by a 2018 NARSAD Young Investigator Grant from the Brain and Behavior Research Foundation [Ref: 27404; awardee: Dr David M Howard] and by a John, Margaret, Alfred and Stewart Sim Fellowship from the Royal College of Physicians of Edinburgh (Awardee: Dr Heather C Whalley). The LBC1936 is supported by the Biotechnology and Biological Sciences Research Council, and the Economic and Social Research Council [BB/W008793/1] (which supports SEH, and JC), Age UK (Disconnected Mind project), the Milton Damerel Trust, the Medical Research Council [G0701120, G1001245, MR/M013111/1, MR/R024065/1] and the University of Edinburgh. Methylation typing of LBC1936 was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. HS is supported by funding from the Wellcome Trust 4-year PhD in Translational Neuroscience [218493/Z/19/Z]. SRC is also supported by a Sir Henry Dale Fellowship jointly funded by Wellcome and the Royal Society [221890/Z/20/Z]. High-performance computing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).' article_number: vbag231 article_processing_charge: Yes article_type: original author: - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Hannah M full_name: Smith, Hannah M last_name: Smith - first_name: Daniel L full_name: McCartney, Daniel L last_name: McCartney - first_name: Elena full_name: Bernabeu, Elena last_name: Bernabeu - first_name: Mahdi full_name: Mahmoudi, Mahdi last_name: Mahmoudi - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Janie full_name: Corley, Janie last_name: Corley - first_name: Sarah E full_name: Harris, Sarah E last_name: Harris - first_name: Simon R full_name: Cox, Simon R last_name: Cox - first_name: Riccardo E full_name: Marioni, Riccardo E last_name: Marioni - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: 'Krätschmer I, Smith HM, McCartney DL, et al. MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes. Bioinformatics Advances. 2026;6(1). doi:10.1093/bioadv/vbag231' apa: 'Krätschmer, I., Smith, H. M., McCartney, D. L., Bernabeu, E., Mahmoudi, M., Campbell, A., … Robinson, M. R. (2026). MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes. Bioinformatics Advances. Oxford University Press. https://doi.org/10.1093/bioadv/vbag231' chicago: 'Krätschmer, Ilse, Hannah M Smith, Daniel L McCartney, Elena Bernabeu, Mahdi Mahmoudi, Archie Campbell, Janie Corley, et al. “MAJA: Multivariate Bayesian Model for Discovery of Shared Epigenetic Pathways across Human Phenotypes.” Bioinformatics Advances. Oxford University Press, 2026. https://doi.org/10.1093/bioadv/vbag231.' ieee: 'I. Krätschmer et al., “MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes,” Bioinformatics Advances, vol. 6, no. 1. Oxford University Press, 2026.' ista: 'Krätschmer I, Smith HM, McCartney DL, Bernabeu E, Mahmoudi M, Campbell A, Corley J, Harris SE, Cox SR, Marioni RE, Robinson MR. 2026. MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes. Bioinformatics Advances. 6(1), vbag231.' mla: 'Krätschmer, Ilse, et al. “MAJA: Multivariate Bayesian Model for Discovery of Shared Epigenetic Pathways across Human Phenotypes.” Bioinformatics Advances, vol. 6, no. 1, vbag231, Oxford University Press, 2026, doi:10.1093/bioadv/vbag231.' short: I. Krätschmer, H.M. Smith, D.L. McCartney, E. Bernabeu, M. Mahmoudi, A. Campbell, J. Corley, S.E. Harris, S.R. Cox, R.E. Marioni, M.R. Robinson, Bioinformatics Advances 6 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "Access to the data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org. https://www.ed.ac.uk/lothian-birth-cohorts/data-access-collaboration gives information on the Lothian Birth Cohort data, which are available on request from the Lothian Birth Cohort Study, University of Edinburgh. Data from both cohorts are not publicly available as they contain information that could compromise participant consent and confidentiality.\r\n\r\nSource code is available at https://github.com/medical-genomics-group/MAJA." date_created: 2026-09-22T05:41:01Z date_published: 2026-09-01T00:00:00Z date_updated: 2026-10-06T12:50:50Z day: '01' ddc: - '570' department: - _id: MaRo doi: 10.1093/bioadv/vbag231 external_id: pmid: - '42761413' file: - access_level: open_access checksum: 86849f1b88c47d050be4aa0a40105a97 content_type: application/pdf creator: dernst date_created: 2026-10-06T12:49:18Z date_updated: 2026-10-06T12:49:18Z file_id: '23064' file_name: 2026_BioinformaticsAdvances_Kraetschmer.pdf file_size: 1370368 relation: main_file success: 1 file_date_updated: 2026-10-06T12:49:18Z fulldoi: https://doi.org/10.1093/bioadv/vbag231 has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Bioinformatics Advances publication_identifier: eissn: - 2635-0041 publication_status: published publisher: Oxford University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'MAJA: Multivariate Bayesian model for discovery of shared epigenetic pathways across human phenotypes' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22963' abstract: - lang: eng text: Although studies of tumor invasion have mainly emphasized the evolution of genetic and epigenetic heterogeneity, cellular behaviors also depend on the physical microenvironment. Yet, the tumor microenvironment is both complex and continuously remodeled, making it hard to rigorously test its causal influence on tumor dissemination. Here, we adopted a reductionist approach to studying tumor cell invasion in microengineered environments of tunable patterned geometries. We find that not only the presence of obstacles but more unexpectedly their spatial disorder causes a drastic shift from a collective to a single-cell mode of invasion—comparable in strength to loss of cell-cell adhesion. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell dissemination results both from local geometrical constraints and a global integration of spatial disorder over time. We identify generic universality classes of invasion dynamics dependent on environmental geometry, enabling us to identify quantitative physical principles for tumor dissemination. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'We thank all the members of the Hannezo and Sixt groups for fruitful discussions and t. Kato for advice on the experimental setup. We are also thankful for support from the Scientific Service Units (SSU) of IST Austria through resources provided by the imaging and Optics Facility (iOF) and the Lab Support Facility (lSF). We used chatGPt (GPt- 5,OpenAi, 2025) to make minor grammatical and stylistic revisions to the original manuscript, which was written by us. We carefully reviewed and verified all changes and are solely responsible for all scientific content, data, interpretation, and conclusions. Funding: Z.D. has received funding from the Doctoral Programme of the Austrian Academy of Sciences (OeAW):grant agreement 26360. this work was supported by the European Research council (grant ERC- SyG 101071793 to M.S.). E.S. and R.P.J. are supported by the Francis Crick Institute, which receives its core funding from cancer Research UK (cc2040), the UK Medical Research council(cc2040), and the Wellcome trust (cc2040) and the European Research council (ERC Advanced Grant cAn_ORGAniSe, grant agreement number 101019366).' article_number: eaed0587 article_processing_charge: Yes article_type: original author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Robert P. full_name: Jenkins, Robert P. last_name: Jenkins - first_name: Erik full_name: Sahai, Erik last_name: Sahai - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. Science Advances. 2026;12(37). doi:10.1126/sciadv.aed0587 apa: Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Jenkins, R. P., Sahai, E., … Hannezo, E. B. (2026). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aed0587 chicago: Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Robert P. Jenkins, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” Science Advances. AAAS, 2026. https://doi.org/10.1126/sciadv.aed0587. ieee: Z. Dunajova et al., “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” Science Advances, vol. 12, no. 37. AAAS, 2026. ista: Dunajova Z, Tasciyan S, Majek J, Merrin J, Jenkins RP, Sahai E, Sixt MK, Hannezo EB. 2026. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. Science Advances. 12(37), eaed0587. mla: Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” Science Advances, vol. 12, no. 37, eaed0587, AAAS, 2026, doi:10.1126/sciadv.aed0587. short: Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, R.P. Jenkins, E. Sahai, M.K. Sixt, E.B. Hannezo, Science Advances 12 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: ' All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials and the associated data and code repositories. Source data underlying all figures and supplementary figures have been deposited in a Zenodo repository (DOi: 10.5281/zenodo.21718217) and will be made publicly available upon publication. custom simulation and analysis codes used in this study are available at https://codeocean.com/capsule/1237446/tree. no unique biological materials were generated in this study. Microfluidic mask designs generated for this work are available from the corresponding authors upon reasonable request.' date_created: 2026-09-20T22:01:48Z date_published: 2026-09-09T00:00:00Z date_updated: 2026-10-06T11:36:34Z day: '09' ddc: - '570' department: - _id: EdHa - _id: MiSi - _id: GradSch - _id: AnSa - _id: NanoFab doi: 10.1126/sciadv.aed0587 external_id: pmid: - '42715298' file: - access_level: open_access checksum: 79f419b659650a39b3dfa58c782690a8 content_type: application/pdf creator: dernst date_created: 2026-10-06T11:30:48Z date_updated: 2026-10-06T11:30:48Z file_id: '23062' file_name: 2026_ScienceAdv_Dunajova.pdf file_size: 11691064 relation: main_file success: 1 file_date_updated: 2026-10-06T11:30:48Z fulldoi: https://doi.org/10.1126/sciadv.aed0587 has_accepted_license: '1' intvolume: ' 12' issue: '37' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments - _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd grant_number: '101071793' name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces' publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: AAAS quality_controlled: '1' related_material: record: - id: '21427' relation: earlier_version status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Substrate heterogeneity promotes cancer cell dissemination through interface roughening tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2026' ...