--- OA_place: repository OA_type: green _id: '21135' abstract: - lang: eng text: Three-dimensional (3D) microscopy data is often anisotropic with significantly lower resolution (up to 8x) along the z axis than along the xy axes. Computationally generating plausible isotropic resolution from anisotropic imaging data would benefit the visual analysis of large-scale volumes. This paper proposes niiv, a self-supervised method for isotropic reconstruction of 3D microscopy data that can quickly produce images at arbitrary output resolutions. The representation embeds a learned latent code within a neural field that describes the implicit higher-resolution isotropic image region. We use an attention-guided latent interpolation approach, which allows flexible information exchange over a local latent neighborhood. Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution lateral image pairs to reconstruct an isotropic volume from low-resolution axial images. We evaluate our method on simulated and real anisotropic electron (EM) and light microscopy (LM) data. Compared to diffusion-based baselines, niiv shows improved reconstruction quality (+1 dB PSNR) and is over three orders of magnitude faster (1,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume in 2/10th of a second, renderable at varying (continuous) high resolutions for display. Our code is available at https://github.com/jakobtroidl/niiv-miccai. acknowledgement: This work was supported by NIH grants 1U01NS132158 and R01HD104969. We thank the reviewers for their constructive feedback. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jakob full_name: Troidl, Jakob last_name: Troidl - first_name: Yiqing full_name: Liang, Yiqing last_name: Liang - first_name: Johanna full_name: Beyer, Johanna last_name: Beyer - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Markus full_name: Hadwiger, Markus last_name: Hadwiger - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: James full_name: Tompkin, James last_name: Tompkin citation: ama: 'Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In: 1st International Workshop on Efficient Medical Artificial Intelligence. Vol 16318. Springer Nature; 2026:257-267. doi:10.1007/978-3-032-13961-0_26' apa: 'Troidl, J., Liang, Y., Beyer, J., Tavakoli, M., Danzl, J. G., Hadwiger, M., … Tompkin, J. (2026). niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In 1st International Workshop on Efficient Medical Artificial Intelligence (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature. https://doi.org/10.1007/978-3-032-13961-0_26' chicago: 'Troidl, Jakob, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann G Danzl, Markus Hadwiger, Hanspeter Pfister, and James Tompkin. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” In 1st International Workshop on Efficient Medical Artificial Intelligence, 16318:257–67. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-13961-0_26.' ieee: 'J. Troidl et al., “niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction,” in 1st International Workshop on Efficient Medical Artificial Intelligence, Daejeon, South Korea, 2026, vol. 16318, pp. 257–267.' ista: 'Troidl J, Liang Y, Beyer J, Tavakoli M, Danzl JG, Hadwiger M, Pfister H, Tompkin J. 2026. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. 1st International Workshop on Efficient Medical Artificial Intelligence. EMA4MICCAI: Efficient Medical Artificial Intelligence, LNCS, vol. 16318, 257–267.' mla: 'Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” 1st International Workshop on Efficient Medical Artificial Intelligence, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:10.1007/978-3-032-13961-0_26.' short: J. Troidl, Y. Liang, J. Beyer, M. Tavakoli, J.G. Danzl, M. Hadwiger, H. Pfister, J. Tompkin, in:, 1st International Workshop on Efficient Medical Artificial Intelligence, Springer Nature, 2026, pp. 257–267. conference: end_date: 2025-09-23 location: Daejeon, South Korea name: 'EMA4MICCAI: Efficient Medical Artificial Intelligence' start_date: 2025-09-23 date_created: 2026-02-01T23:01:44Z date_published: 2026-01-03T00:00:00Z date_updated: 2026-02-16T08:50:50Z day: '03' department: - _id: JoDa doi: 10.1007/978-3-032-13961-0_26 intvolume: ' 16318' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.09.07.611785 month: '01' oa: 1 oa_version: Preprint page: 257-267 publication: 1st International Workshop on Efficient Medical Artificial Intelligence publication_identifier: eissn: - 1611-3349 isbn: - '9783032139603' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/jakobtroidl/niiv-miccai scopus_import: '1' status: public title: 'niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16318 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21767' abstract: - lang: eng text: 'The involvement of non-scientific staff in discussions about animal welfare and scientific quality is essential for biomedical research progress. In this study, we developed a survey to collect the self-perception of animal care staff (ACS) and laboratory technicians about their involvement in scientific planning and conduct. Participants were contacted to complete an anonymous online questionnaire. We obtained 850 responses, mainly from Europe: 564 from ACS and 286 from laboratory technicians. Job satisfaction was assessed as positive by ACS and laboratory technicians despite the low frequency of culture of care activities and mental health meetings. Both groups expressed their desire to be trained in research planning and conduct; however, regular training was not reported. In addition, the inability to act on animal welfare concerns owing to experimental reasons was reported by both groups. Over half of the participants felt valued and appreciated by the lead scientists or animal facility manager; however, it is not clear how they are acknowledged, as their names on the authors list or in the manuscript acknowledgments are barely included. Our results indicated that involvement of ACS and laboratory technicians in planning and conducting studies would improve their understanding of how experiments are done, and therefore communication processes, work satisfaction, animal welfare, and scientific quality. Finally, we provided recommendations to improve the engagement of ACS and laboratory technicians in discussions about animal research planning and conduct.' - lang: fre text: 'La participation de personnel non-scientifique aux discussions sur le bien-être animal et la qualité scientifique est essentielle aux progrès la recherche biomédicale. Dans cette étude, nous avons développé une enquête pour recueillir l''auto-perception du personnel chargé des soins prodigués aux animaux (PCSA) et des techniciens de laboratoire (TL) sur leur implication dans la planification et la conduite scientifiques. Les participants ont été contactés pour remplir un questionnaire anonyme en ligne. Nous avons obtenu 850 réponses, principalement en Europe : 564 provenant de PCSA et 286 de TL. La satisfaction au travail a été évaluée comme positive par le PCSA et les TL malgré la faible fréquence d’activités sur la culture des soins et de réunions concernant la santé mentale. Bien que les deux groupes aient exprimé leur désir d''être formés à la planification et à la conduite de la recherche, aucune formation réelle régulière n''a été signalée. De plus, l''incapacité d''agir sur les préoccupations relatives au bien-être animal pour des raisons expérimentales a été signalée par les deux groupes. Plus de la moitié des participants se sont sentis valorisés et appréciés par les scientifiques principaux ou le gestionnaire de l’installation animale mais on ne sait pas clairement comment ils sont reconnus, car leurs noms sur la liste des auteurs ou dans les remerciements sont à peine inclus dans la documentation. Nos résultats ont indiqué que la participation du PCSA et des TL à la planification et à la conduite des études améliorerait leur compréhension de la façon dont les expériences sont effectuées et, par conséquent, les processus de communication, leur satisfaction au travail ainsi que le bien-être animal et la qualité scientifique. Enfin, nous avons formulé des recommandations pour améliorer la participation du PCSA et des TL aux discussions sur la planification et la conduite de la recherche animale.' - lang: ger text: 'Die Einbeziehung von nichtwissenschaftlichem Personal in Diskussionen über Tierschutz und wissenschaftliche Qualität ist für Fortschritte in biomedizinischer Forschung von entscheidender Bedeutung. In dieser Studie haben wir eine Umfrage entwickelt, um die Selbsteinschätzung von Tierpflegern (ACS) und Labortechnikern (LT) hinsichtlich ihrer Beteiligung an der wissenschaftlichen Planung und Durchführung zu erfassen. Die Teilnehmer wurden gebeten, einen anonymen Online-Fragebogen auszufüllen. Wir erhielten 850 Rückmeldungen, hauptsächlich aus Europa: 564 von ACS und 286 von LT. Die Arbeitszufriedenheit wurde von ACS und LT trotz der geringen Häufigkeit von Pflegeaktivitäten und Treffen zum Thema psychische Gesundheit als positiv bewertet. Beide Gruppen äußerten den Wunsch, in der Forschungsplanung und -durchführung geschult zu werden, doch regelmäßig stattfindende Schulungen wurden nicht berichtet. Außerdem wurde von beiden Gruppen vermeldet, dass sie aus versuchstechnischen Gründen nicht in der Lage waren, auf Tierschutzbedenken zu reagieren. Über die Hälfte der Teilnehmer fühlte sich von den leitenden Wissenschaftlern oder dem Leiter der Tierhaltungseinrichtung geschätzt und anerkannt; es ist jedoch unklar, inwiefern sie wirklich gewürdigt werden, da ihre Namen kaum in der Autorenliste oder in den Danksagungen des Manuskripts aufgeführt sind. Unsere Ergebnisse deuteten darauf hin, dass die Einbeziehung von ACS und LT in die Planung und Durchführung von Studien ihr Verständnis für die Durchführung von Experimenten verbessern würde – und damit auch Kommunikationsprozesse, Arbeitszufriedenheit, Tierwohl und wissenschaftliche Qualität. Abschließend gaben wir Empfehlungen zur Verbesserung der Einbeziehung von ACS und LT in Diskussionen über die Planung und Durchführung von Tierversuchen.' - lang: spa text: 'La participación del personal no científico en los debates sobre el bienestar animal y la calidad científica es fundamental para el avance de la investigación biomédica. En este estudio, desarrollamos una encuesta para recoger la autopercepción del personal encargado del cuidado de los animales (ACS) y de los técnicos de laboratorio (LT) sobre su implicación en la planificación y la realización científicas. Se contactó con los participantes para que cumplimentaran un cuestionario anónimo en línea. Obtuvimos 850 respuestas, principalmente de Europa: 564 de ACS y 286 de LT. La satisfacción laboral fue evaluada como positiva por ACS y técnicos de laboratorio a pesar de la baja frecuencia de actividades de cultura del cuidado y reuniones sobre bienestar mental. Ambos grupos expresaron su deseo de recibir formación en planificación y realización de investigaciones, sin embargo, no se informó sobre una formación regular. Asimismo, ambos grupos señalaron la incapacidad de actuar ante las preocupaciones sobre el bienestar animal por motivos experimentales. Más de la mitad de los participantes se sintieron valorados y apreciados por los científicos principales o el responsable de las instalaciones de animales; sin embargo, no está claro cómo se les reconoce, ya que apenas se incluyen sus nombres en la lista de autores o en los agradecimientos del manuscrito. Nuestros resultados indicaron que la participación de los ACS y los LT en la planificación y realización de los estudios mejoraría su comprensión de cómo se hacen los experimentos y, por tanto, los procesos de comunicación, la satisfacción laboral, el bienestar animal y la calidad científica. Finalmente, proporcionamos recomendaciones para mejorar el compromiso de la AEC y la LT en los debates sobre la planificación y la realización de investigaciones con animales.' acknowledgement: "We deeply acknowledge all the animal care staff and laboratory technicians who participated in this study! We acknowledge Working Groups 1 and 4 from COST Action IMPROVE (“3Rs concepts to improve the quality of biomedical science”), CA21139, supported by COST (European Cooperation in Science and Technology) for their feedback and support. We also acknowledge Aoife Milford for her comments and contributions to the final draft of the manuscript.\r\nThis publication was based on work from the COST Action IMPROVE (“3Rs concepts to improve the quality of biomedical science”), CA21139, supported by COST (European Cooperation in Science and Technology)." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Fernando full_name: Gonzalez-Uarquin, Fernando last_name: Gonzalez-Uarquin - first_name: Paulin full_name: Jirkof, Paulin last_name: Jirkof - first_name: Bettina full_name: Bert, Bettina last_name: Bert - first_name: Penny full_name: Hawkins, Penny last_name: Hawkins - first_name: Ljupco full_name: Angelovski, Ljupco last_name: Angelovski - first_name: Jan full_name: Baumgart, Jan last_name: Baumgart - first_name: Nadine full_name: Baumgart, Nadine last_name: Baumgart - first_name: Özge S. full_name: Cevik, Özge S. last_name: Cevik - first_name: Nuno H. full_name: Franco, Nuno H. last_name: Franco - first_name: Erdal full_name: Horata, Erdal last_name: Horata - first_name: Rohish full_name: Kaura, Rohish last_name: Kaura - first_name: Winfried full_name: Neuhaus, Winfried last_name: Neuhaus - first_name: Brigida full_name: Riso, Brigida last_name: Riso - first_name: Adrian J. full_name: Smith, Adrian J. last_name: Smith - first_name: Athanassia full_name: Sotiropoulos, Athanassia last_name: Sotiropoulos - first_name: Augusto full_name: Vitale, Augusto last_name: Vitale - first_name: Sophie full_name: Schober, Sophie id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8 last_name: Schober citation: ama: 'Gonzalez-Uarquin F, Jirkof P, Bert B, et al. Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals. 2026. doi:10.1177/00236772251400976' apa: 'Gonzalez-Uarquin, F., Jirkof, P., Bert, B., Hawkins, P., Angelovski, L., Baumgart, J., … Schober, S. (2026). Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals. SAGE Publications. https://doi.org/10.1177/00236772251400976' chicago: 'Gonzalez-Uarquin, Fernando, Paulin Jirkof, Bettina Bert, Penny Hawkins, Ljupco Angelovski, Jan Baumgart, Nadine Baumgart, et al. “Building Bridges: Involvement of Animal Care Staff and Laboratory Technicians in Experimental Planning and Conduct of Animal Studies for Better Job Satisfaction and Science.” Laboratory Animals. SAGE Publications, 2026. https://doi.org/10.1177/00236772251400976.' ieee: 'F. Gonzalez-Uarquin et al., “Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science,” Laboratory Animals. SAGE Publications, 2026.' ista: 'Gonzalez-Uarquin F, Jirkof P, Bert B, Hawkins P, Angelovski L, Baumgart J, Baumgart N, Cevik ÖS, Franco NH, Horata E, Kaura R, Neuhaus W, Riso B, Smith AJ, Sotiropoulos A, Vitale A, Schober S. 2026. Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals.' mla: 'Gonzalez-Uarquin, Fernando, et al. “Building Bridges: Involvement of Animal Care Staff and Laboratory Technicians in Experimental Planning and Conduct of Animal Studies for Better Job Satisfaction and Science.” Laboratory Animals, SAGE Publications, 2026, doi:10.1177/00236772251400976.' short: F. Gonzalez-Uarquin, P. Jirkof, B. Bert, P. Hawkins, L. Angelovski, J. Baumgart, N. Baumgart, Ö.S. Cevik, N.H. Franco, E. Horata, R. Kaura, W. Neuhaus, B. Riso, A.J. Smith, A. Sotiropoulos, A. Vitale, S. Schober, Laboratory Animals (2026). date_created: 2026-04-26T22:01:47Z date_published: 2026-04-14T00:00:00Z date_updated: 2026-06-18T08:33:36Z day: '14' ddc: - '570' department: - _id: PreCl doi: 10.1177/00236772251400976 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1177/00236772251400976 month: '04' oa: 1 oa_version: Published Version publication: Laboratory Animals publication_identifier: eissn: - 1758-1117 issn: - 0023-6772 publication_status: epub_ahead publisher: SAGE Publications quality_controlled: '1' scopus_import: '1' status: public title: 'Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '21949' abstract: - lang: eng text: "Cardiac T1 mapping provides critical quantitative insights into myocardial tissue composition, enabling the assessment of pathologies such as fibrosis, inflammation, and edema.\r\nHowever, the inherently dynamic nature of the heart imposes strict limits on acquisition\r\ntimes, making high-resolution T1 mapping a persistent challenge. Compressed sensing (CS)\r\napproaches have reduced scan durations by undersampling k-space and reconstructing images from partial data, and recent studies show that jointly optimizing the undersampling\r\npatterns with the reconstruction network can substantially improve performance. Still,\r\nmost current T1 mapping pipelines rely on static, hand-crafted masks that do not exploit\r\nthe full acceleration and accuracy potential. Furthermore, most existing methods do not\r\nlevarage the physical T1 decay model in optimization. In this work, we introduce T1-\r\nPILOT: an end-to-end method that explicitly incorporates the T1 signal relaxation model\r\ninto the sampling–reconstruction framework to guide the learning of non-Cartesian trajectories, cross-frame alignment, and T1 decay estimation. Through extensive experiments\r\non the CMRxRecon dataset, T1-PILOT significantly outperforms several baseline strategies (including learned single-mask and fixed radial or golden-angle sampling schemes),\r\nachieving higher T1 map fidelity at greater acceleration factors. In particular, we observe consistent gains in PSNR and VIF relative to existing methods, along with marked\r\nimprovements in delineating finer myocardial structures. Our results highlight that optimizing sampling trajectories in tandem with the physical relaxation model leads to both\r\nenhanced quantitative accuracy and reduced acquisition times. Code for reproducing all\r\nexperiments and results is available at https://github.com/tamirshor7/T1-PILOT" alternative_title: - PMLR article_processing_charge: No author: - first_name: Tamir full_name: Shor, Tamir last_name: Shor - first_name: Moti full_name: Freiman, Moti last_name: Freiman - first_name: Chaim full_name: Baskin, Chaim last_name: Baskin - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: 'Shor T, Freiman M, Baskin C, Bronstein AM. T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. In: Medical Imaging with Deep Learning. Vol 315. ML Research Press; :1969-1982.' apa: 'Shor, T., Freiman, M., Baskin, C., & Bronstein, A. M. (n.d.). T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. In Medical Imaging with Deep Learning (Vol. 315, pp. 1969–1982). Taipei, Taiwan: ML Research Press.' chicago: 'Shor, Tamir, Moti Freiman, Chaim Baskin, and Alex M. Bronstein. “T1-PILOT: Physics-Informed Learned Optimized Trajectories for T1 Mapping Acceleration.” In Medical Imaging with Deep Learning, 315:1969–82. ML Research Press, n.d.' ieee: 'T. Shor, M. Freiman, C. Baskin, and A. M. Bronstein, “T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration,” in Medical Imaging with Deep Learning, Taipei, Taiwan, vol. 315, pp. 1969–1982.' ista: 'Shor T, Freiman M, Baskin C, Bronstein AM. T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. Medical Imaging with Deep Learning. MIDL: Medical Imaging with Deep Learning, PMLR, vol. 315, 1969–1982.' mla: 'Shor, Tamir, et al. “T1-PILOT: Physics-Informed Learned Optimized Trajectories for T1 Mapping Acceleration.” Medical Imaging with Deep Learning, vol. 315, ML Research Press, pp. 1969–82.' short: T. Shor, M. Freiman, C. Baskin, A.M. Bronstein, in:, Medical Imaging with Deep Learning, ML Research Press, n.d., pp. 1969–1982. conference: end_date: 2026-07-10 location: Taipei, Taiwan name: 'MIDL: Medical Imaging with Deep Learning' start_date: 2026-07-08 corr_author: '1' date_created: 2026-06-07T22:01:36Z date_published: 2026-03-17T00:00:00Z date_updated: 2026-06-08T08:05:24Z day: '17' ddc: - '000' department: - _id: AlBr has_accepted_license: '1' intvolume: ' 315' keyword: - Cardiac T1 Mapping - Trajectory Optimization and Reconstruction - PhysicsInformed Deep-Learning language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://openreview.net/forum?id=nZaPtHbd6N#discussion month: '03' oa: 1 oa_version: Published Version page: 1969-1982 publication: Medical Imaging with Deep Learning publication_identifier: eissn: - 2640-3498 publication_status: accepted publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/tamirshor7/T1-PILOT scopus_import: '1' status: public title: 'T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 315 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22607' abstract: - lang: eng text: "Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\".\r\nCode: https://github.com/madvorak/duality/tree/v3.2.0" acknowledgement: "We would like to thank David Bartl and Jasmin Blanchette for frequent consultations.\r\nWe would also like to express gratitude to Henrik Böving for a help with generalization\r\nfrom extended rationals to extended linearly ordered fields and to Andrew Yang for the\r\nproof of Finset.univ_sum_of_zero_when_not. We would also like to acknowledge Antoine\r\nChambert-Loir, Apurva Nakade, Yaël Dillies, Richard Copley, Edward van de Meent, Markus\r\nHimmel, Mario Carneiro, and Kevin Buzzard." article_number: '14253' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2026;2. doi:10.46298/afm.14253 apa: Dvorak, M., & Kolmogorov, V. (2026). Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. EPI Sciences. https://doi.org/10.46298/afm.14253 chicago: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics. EPI Sciences, 2026. https://doi.org/10.46298/afm.14253. ieee: M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” Annals of Formalized Mathematics, vol. 2. EPI Sciences, 2026. ista: Dvorak M, Kolmogorov V. 2026. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2, 14253. mla: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics, vol. 2, 14253, EPI Sciences, 2026, doi:10.46298/afm.14253. short: M. Dvorak, V. Kolmogorov, Annals of Formalized Mathematics 2 (2026). corr_author: '1' das_tickbox: '0' date_created: 2026-07-29T09:06:55Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-07-29T10:50:17Z day: '13' ddc: - '500' department: - _id: VlKo - _id: GradSch doi: 10.46298/afm.14253 external_id: arxiv: - '2409.08119' has_accepted_license: '1' intvolume: ' 2' keyword: - Farkas lemma - linear programming - extended reals - calculus of inductive constructions language: - iso: eng mathsc: - 68V20 - 15A39 - 90C05 month: '03' oa_version: Published Version publication: Annals of Formalized Mathematics publication_identifier: eissn: - 3117-4604 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '20071' relation: earlier_version status: public researchdata_availability: no status: public supplementarymaterial: no title: Duality theory in linear optimization and its extensions -- formally verified 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: 2 year: '2026' ... --- OA_place: repository _id: '22242' abstract: - lang: eng text: This deposit contains the data and analysis code accompanying the publication "Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices" (Borovkov et al.). The deposit includes the raw transport and current-noise measurements of three gate-defined quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise (flank-method) analysis with the pointers linking every analyzed PSD trace to the raw data, the toy-model noise simulation datasets behind the supplementary figures, the archived analysis figures (PSD fits and lever-arm extractions), and the Python code reproducing the full analysis and all figures. The code is also maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions are provided in the README files. acknowledged_ssus: - _id: M-Shop - _id: NanoFab article_processing_charge: No author: - first_name: Maksim full_name: Borovkov, Maksim id: 1fd0975f-8b61-11ed-b69e-d149334f28c5 last_name: Borovkov citation: ama: Borovkov M. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. 2026. doi:10.15479/AT-ISTA-22242 apa: Borovkov, M. (2026). Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22242 chicago: Borovkov, Maksim. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22242. ieee: M. Borovkov, “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. ista: Borovkov M. 2026. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22242. mla: Borovkov, Maksim. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22242. short: M. Borovkov, (2026). contributor: - contributor_type: contact_person first_name: Maksim id: 1fd0975f-8b61-11ed-b69e-d149334f28c5 last_name: Borovkov corr_author: '1' date_created: 2026-07-04T17:32:27Z date_published: 2026-07-04T00:00:00Z date_updated: 2026-08-03T11:08:38Z day: '04' ddc: - '530' department: - _id: GradSch - _id: GeKa doi: 10.15479/AT-ISTA-22242 doi_confirm: '1' file: - access_level: open_access checksum: 2a1ea297e01a7a202a6b144d69a46eef content_type: application/x-zip-compressed creator: mborovko date_created: 2026-07-04T17:28:49Z date_updated: 2026-07-04T17:28:49Z file_id: '22243' file_name: noise_paper_public_deposit.zip file_size: 3082596099 relation: main_file success: 1 file_date_updated: 2026-07-04T17:28:49Z has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version project: - _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811 grant_number: '101115315' name: Quantum bits with Kitaev Transmons - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3 grant_number: '101150858' name: Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium - _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f grant_number: PAT 7682124 name: Superconducting spin qubits in planar Ge publisher: Institute of Science and Technology Austria related_material: link: - relation: research_data url: https://github.com/ISTA-Nanoelectronics/noise_paper_public record: - id: '22619' relation: used_in_publication status: public status: public title: Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22647' abstract: - lang: eng text: "Within the plant endomembrane system, the vesicle coat protein clathrin localizes to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE). While the role of clathrin in endocytosis at the PM is well established, its function at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell surface) or en route to the vacuole, is debated. Similarly debated are potential homeostatic mechanisms balancing the trafficking routes, especially endocytosis and late secretion.\r\nWe address these questions in Arabidopsis thaliana using conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants.\r\nCHC silencing interferes with trafficking of cargoes destined for the apoplast and the PM, supporting a function of clathrin in late secretion. The secretory cargoes become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing, overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis while secretion continues normally at early points of induction. Conversely, secretory mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE endocytic component.\r\nTogether, our data show a role of clathrin in secretion and suggest secretion as a fundamental trafficking process to which endocytosis is adjusted by a weak homeostatic mechanism." acknowledgement: 'The authors wish to acknowledge Dr. Paweł Baster for cloning PIN1-GFP-2/pDONR221, Ms. Aline Monzer and Dr. Mingyue Li for help with CHC protein level evaluation, Dr. Michał Rychłowski for help with confocal microscopy, Prof. Ari Pekka Mähönen for sharing the p1R4-pUBQ10:XVE plasmid, and Prof. Ying Gu for sharing seeds of the sec5 mutant. M.A. would like to thank Dr. Xixi Zhang and Prof. Sebastian Bednarek for inspiring discussions. This work was supported by the Taif University Researchers Supporting Project, TURSP-HC2022/02 to JF and SA and Austrian Science Fund (FWF): I 3630-B25 to JF. Open Access funding provided by Institute of Science and Technology Austria.' article_number: nph.71454 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Adam full_name: Gackowski, Adam last_name: Gackowski - first_name: Ivana full_name: Matijevic, Ivana id: 83c17ce3-15b2-11ec-abd3-f486545870bd last_name: Matijevic - first_name: Saqer S. full_name: Alotaibi, Saqer S. last_name: Alotaibi - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. 2026. doi:10.1111/nph.71454 apa: Adamowski, M., Gackowski, A., Matijevic, I., Alotaibi, S. S., & Friml, J. (2026). The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. Wiley. https://doi.org/10.1111/nph.71454 chicago: Adamowski, Maciek, Adam Gackowski, Ivana Matijevic, Saqer S. Alotaibi, and Jiří Friml. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71454. ieee: M. Adamowski, A. Gackowski, I. Matijevic, S. S. Alotaibi, and J. Friml, “The role of clathrin in post‐Golgi secretion in plant cells,” New Phytologist. Wiley, 2026. ista: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. 2026. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist., nph. 71454. mla: Adamowski, Maciek, et al. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist, nph. 71454, Wiley, 2026, doi:10.1111/nph.71454. short: M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: 'Original data associated with this study have been deposited in Dataset S1. The accession nos. of A. thaliana genes used in this study are as follows: CHC1 (AT3G11130), CHC2 (AT3G08530), CLC2 (AT2G40060), TPLATE (AT3G01780), AP2A1 (AT5G22770), DRP1C (AT1G14830), GNOM-LIKE1 (AT5G39500), BEN3/BIG2 (AT3G60860), TMK4 (AT3G23750), PIN1 (AT1G73590), AUXILIN-LIKE1 (AT4G12780), AP1M2 (AT1G60780), ECHIDNA (AT1G09330), SEC5A (AT1G76850), SEC5B (AT1G21170), TUB2 (AT5G62690), and PP2AA3 (AT1G13320).' date_created: 2026-08-04T06:48:41Z date_published: 2026-07-20T00:00:00Z date_updated: 2026-08-04T07:58:27Z day: '20' department: - _id: JiFr - _id: MaLo - _id: GradSch doi: 10.1111/nph.71454 external_id: pmid: - '42477503' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.71454 month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: epub_ahead publisher: Wiley quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: The role of clathrin in post‐Golgi secretion in plant cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: gold _id: '21668' abstract: - lang: eng text: "This artifact allows to review and reproduce the experiments from the paper *A Revised Practitioner's Guide to MDP Model Checking Algorithms*.\r\nThe package contains all original logfiles and derived data used to generate the plots as in the paper. Furthermore, the artifact contains the model checking tools `Storm` and `mcsta` in the version exercised in the paper, the used Docker container, as well as benchmark instances and execution scripts to reproduce the experiments.\r\n\r\nSee also the artifact of the conference paper: https://zenodo.org/records/7509474" article_processing_charge: No author: - first_name: Arnd full_name: Hartmanns, Arnd last_name: Hartmanns - first_name: Sebastian full_name: Junges, Sebastian last_name: Junges - first_name: Tim full_name: Quatmann, Tim last_name: Quatmann - first_name: Maximilian full_name: Weininger, Maximilian id: 02ab0197-cc70-11ed-ab61-918e71f56881 last_name: Weininger orcid: 0000-0002-0163-2152 citation: ama: Hartmanns A, Junges S, Quatmann T, Weininger M. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. 2025. doi:10.5281/ZENODO.14500423 apa: Hartmanns, A., Junges, S., Quatmann, T., & Weininger, M. (2025). Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. Zenodo. https://doi.org/10.5281/ZENODO.14500423 chicago: Hartmanns, Arnd, Sebastian Junges, Tim Quatmann, and Maximilian Weininger. “Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.14500423. ieee: A. Hartmanns, S. Junges, T. Quatmann, and M. Weininger, “Benchmark data for the revised practitioner’s guide to MDP model checking algorithms.” Zenodo, 2025. ista: Hartmanns A, Junges S, Quatmann T, Weininger M. 2025. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms, Zenodo, 10.5281/ZENODO.14500423. mla: Hartmanns, Arnd, et al. Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms. Zenodo, 2025, doi:10.5281/ZENODO.14500423. short: A. Hartmanns, S. Junges, T. Quatmann, M. Weininger, (2025). date_created: 2026-04-07T09:47:22Z date_published: 2025-03-07T00:00:00Z date_updated: 2026-04-07T09:52:55Z day: '07' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.14500423 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.14500423 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '21661' relation: used_for_analysis_in status: public status: public title: Benchmark data for the revised practitioner's guide to MDP model checking algorithms type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '15128' abstract: - lang: eng text: We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\zeta)$ and a general class of related quantities involving two resolvents at nearby spectral parameters. - lang: fre text: "On établit un théorème limite central universel pour les statistiques linéaires mésoscopiques des valeurs propres d’une matrice de type Wigner au milieu du spectre, avec des fonctions de classe \r\n et à support compact. La principale nouveauté de cette approche est qu’elle repose sur une loi locale optimale pour la fonction à deux points $T(z,\\zeta)$ , ainsi que pour une classe plus générale d’observables impliquant deux résolvantes évaluées en des paramètres proches." acknowledgement: "I would like to express my gratitude to László Erdős for suggesting the project and supervising my work. I am also thankful to Yuanyuan Xu and Oleksii Kolupaiev for many helpful discussions. Furthermore, I am grateful to Guillaume Dubach for translating the abstract into French.\r\nThe author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov citation: ama: Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2025;61(1):129-154. doi:10.1214/23-AIHP1438 apa: Riabov, V. (2025). Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AIHP1438 chicago: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/23-AIHP1438. ieee: V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1. Institute of Mathematical Statistics, pp. 129–154, 2025. ista: Riabov V. 2025. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 61(1), 129–154. mla: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1, Institute of Mathematical Statistics, 2025, pp. 129–54, doi:10.1214/23-AIHP1438. short: V. Riabov, Annales de l’institut Henri Poincare (B) Probability and Statistics 61 (2025) 129–154. corr_author: '1' date_created: 2024-03-20T09:41:04Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-05-19T13:54:31Z day: '01' department: - _id: GradSch - _id: LaEr doi: 10.1214/23-AIHP1438 ec_funded: 1 external_id: arxiv: - '2301.01712' isi: - '001427953600004' intvolume: ' 61' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.01712 month: '02' oa: 1 oa_version: Preprint page: 129-154 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annales de l'institut Henri Poincare (B) Probability and Statistics publication_identifier: issn: - 0246-0203 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Mesoscopic eigenvalue statistics for Wigner-type matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2025' ... --- OA_place: publisher _id: '19033' abstract: - lang: eng text: "This data set contains the simulation input files, scripts, and figures data belonging to the publication\r\n\r\nAlberto Scacchi, Carlo Rigoni, Mikko P. Haataja, Jakko V. I. Timonen, and Maria Sammalkorpi, \"A Coarse-grained Model for Aqueous Two-phase Systems: Application to Ferrofluids\", Journal of Colloids and Interface Science (2025). https://doi.org/10.1016/j.jcis.2025.01.256." acknowledgement: This work was supported by the Swiss National Science Foundation under the project no. P500PT_206916 (A.S.) and the Academy of Finland through its Centres of Excellence Programs (2022-2029, LIBER) under projects no. 346111 and 364205 (M.S.) and 346112 and 364206 (J.T.). MPH was supported by the National Science Foundation through the Princeton University (PCCM) Materials Research Science and Engineering Center DMR-2011750. A.S. warmly thanks Bob Evans for extensive scientific discussions and for his hospitality during the research visit in Bristol. Computational resources by CSC IT Centre for Finland, the Aalto Science-IT project, and RAMI -- RawMatters Finland Infrastructure are also gratefully acknowledged. article_processing_charge: No author: - first_name: Alberto full_name: Scacchi, Alberto last_name: Scacchi citation: ama: Scacchi A. 2025_SCACCHI_JCIS. 2025. doi:10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1 apa: Scacchi, A. (2025). 2025_SCACCHI_JCIS. Fairdata. https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1 chicago: Scacchi, Alberto. “2025_SCACCHI_JCIS.” Fairdata, 2025. https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1. ieee: A. Scacchi, “2025_SCACCHI_JCIS.” Fairdata, 2025. ista: Scacchi A. 2025. 2025_SCACCHI_JCIS, Fairdata, 10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1. mla: Scacchi, Alberto. 2025_SCACCHI_JCIS. Fairdata, 2025, doi:10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1. short: A. Scacchi, (2025). contributor: - first_name: Carlo id: c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0 last_name: Rigoni - first_name: Maria last_name: Sammalkorpi - first_name: Mikko last_name: Haataja - first_name: Jaakoo last_name: Timonen date_created: 2025-02-17T09:00:36Z date_published: 2025-02-05T00:00:00Z date_updated: 2025-09-30T10:31:44Z day: '05' ddc: - '530' department: - _id: RaKl doi: 10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1 month: '02' oa: 1 oa_version: Published Version publisher: Fairdata related_material: record: - id: '19024' relation: used_in_publication status: public status: public title: 2025_SCACCHI_JCIS 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '19416' abstract: - lang: eng text: 'Recently, Biagioli and Tompkins (2023, https://doi.org/10.1029/2022ms003231) used a simple stochastic model to derive a dimensionless parameter to predict convective self aggregation (SA) development, which was based on the derivation of the maximum free convective distance ($d_{clr}$) expected in the pre-aggregated, random state. Our goal is to test and further investigate this hypothesis, namely that $d_{clr}$ can predict SA occurrence, using an ensemble of twenty-four distinct combinations of horizontal mixing, planetary boundary layer (PBL), and microphysical parameterizations. We conclude that the key impact of parameterization schemes on SA is through their control of the number of convective cores and their relative spacing, $d_{clr}$, which itself is impacted by cold-pool (CP) properties and mean updraft core size. SA is more likely when the convective core count is small, while CPs modify convective spacing via suppression in their interiors and triggering by gust-front convergence and collisions. Each parameterization scheme emphasizes a different mechanism. Subgrid-scale horizontal turbulent mixing mainly affects SA through the determination of convective core size and thus spacing. The sensitivity to the microphysics is mainly through rain evaporation and the subsequent impact on CPs, while perturbations to the ice cloud microphysics have a limited effect. Non-local PBL mixing schemes promote SA primarily by increasing convective inhibition through inversion entrainment and altering low cloud amounts, leading to fewer convective cores and larger $d_{clr}$. ' acknowledgement: This article is based on chapter 3 of AC Ph.D. thesis. The authors thank Graziano Giuliani for his coding assistance. We also thank Daniel Hernández-Deckers, Paolina Cerlini, and especially to Giovanni Biagioli for discussions and feedback. We also thank two reviewers for their insightful comments. AC was supported by a fellowship awarded by ICTP and by the European Union Horizon 2020 Marie Skłodowska-Curie grant agreement No. 101034413. CM acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). article_number: e2024MS004791 article_processing_charge: Yes article_type: original author: - first_name: Alejandro full_name: Casallas Garcia, Alejandro id: 92081129-2d75-11ef-a48d-b04dd7a2385a last_name: Casallas Garcia orcid: 0000-0002-1988-5035 - first_name: A.M. full_name: Tompkins, A.M. last_name: Tompkins - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: G. full_name: Thompson, G. last_name: Thompson citation: ama: Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 2025;17(3). doi:10.1029/2024MS004791 apa: Casallas Garcia, A., Tompkins, A. M., Muller, C. J., & Thompson, G. (2025). Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2024MS004791 chicago: Casallas Garcia, Alejandro, A.M. Tompkins, Caroline J Muller, and G. Thompson. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems. Wiley, 2025. https://doi.org/10.1029/2024MS004791. ieee: A. Casallas Garcia, A. M. Tompkins, C. J. Muller, and G. Thompson, “Sensitivity of self-aggregation and the key role of the free convection distance,” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3. Wiley, 2025. ista: Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. 2025. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 17(3), e2024MS004791. mla: Casallas Garcia, Alejandro, et al. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3, e2024MS004791, Wiley, 2025, doi:10.1029/2024MS004791. short: A. Casallas Garcia, A.M. Tompkins, C.J. Muller, G. Thompson, Journal of Advances in Modeling Earth Systems 17 (2025). corr_author: '1' date_created: 2025-03-19T07:58:38Z date_published: 2025-03-18T00:00:00Z date_updated: 2025-09-30T11:04:38Z day: '18' ddc: - '550' department: - _id: CaMu doi: 10.1029/2024MS004791 ec_funded: 1 external_id: isi: - '001447023900001' file: - access_level: open_access checksum: bc32677e63f8abb07b330f4a08da796d content_type: application/pdf creator: acasalla date_created: 2025-03-19T07:58:21Z date_updated: 2025-03-19T07:58:21Z file_id: '19417' file_name: Casallas_et_al_2025_dclr.pdf file_size: 18285343 relation: main_file file_date_updated: 2025-03-19T07:58:21Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Journal of Advances in Modeling Earth Systems publication_identifier: eissn: - 1942-2466 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Sensitivity of self-aggregation and the key role of the free convection distance tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 17 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19443' abstract: - lang: eng text: In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/. acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Pavol full_name: Harar, Pavol id: e03d953a-6e8c-11ef-99e4-f0717d385cd5 last_name: Harar orcid: 0000-0001-5206-1794 - first_name: Lukas full_name: Herrmann, Lukas last_name: Herrmann - first_name: Philipp full_name: Grohs, Philipp last_name: Grohs - first_name: David full_name: Haselbach, David last_name: Haselbach citation: ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4. doi:10.1016/j.str.2025.01.020' apa: 'Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. Elsevier. https://doi.org/10.1016/j.str.2025.01.020' chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure. Elsevier, 2025. https://doi.org/10.1016/j.str.2025.01.020.' ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” Structure, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.' ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.' mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:10.1016/j.str.2025.01.020.' short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4. corr_author: '1' date_created: 2025-03-23T23:01:27Z date_published: 2025-04-03T00:00:00Z date_updated: 2025-09-30T11:13:02Z day: '03' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.str.2025.01.020 external_id: isi: - '001463196100001' pmid: - '39947174' file: - access_level: open_access checksum: f346bc357a66a88cca3d0eb95793fb73 content_type: application/pdf creator: dernst date_created: 2025-08-05T12:15:13Z date_updated: 2025-08-05T12:15:13Z file_id: '20130' file_name: 2025_Structure_Harar.pdf file_size: 4367530 relation: main_file success: 1 file_date_updated: 2025-08-05T12:15:13Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 820-827.e4 pmid: 1 publication: Structure publication_identifier: eissn: - 1878-4186 issn: - 0969-2126 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: software url: https://github.com/paloha/faket/ scopus_import: '1' status: public title: 'FakET: Simulating cryo-electron tomograms with neural style transfer' 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: 33 year: '2025' ... --- OA_place: repository OA_type: green _id: '19771' abstract: - lang: eng text: "This artifact allows to review and reproduce the Isabelle proofs and practical experiments from the paper *Fixed Point Certificates for Reachability and Expected Rewards in MDPs*.\r\nThe contents are two-fold:\r\nFirst, the artifact contains a formally verified certificate checker for the certificates presented in the paper.\r\nThe formal Isabelle/HOL proofs of the background theory can be inspected, checked by Isabelle and the code extraction can be retraced.\r\n\r\nSecond, the artifact contains a modified version of the model checking tool `Storm` with support for certificate generation. Together with the provided scripts and benchmark files, this allows to reproduce the experiments from the paper.\r\nAn appropriate subset of the experiments is given to allow a review in a timely manner. In addition, original logfiles from our experiments are provided, allowing a detailed inspection.\r\n\r\nThe package includes convenient installation scripts for [the TACAS 2023 VM](https://doi.org/10.5281/zenodo.7113223) (based on Ubuntu 22.04).\r\nA native installation on Linux or macOS systems (including the newer ARM-based machines) is also possible." article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Tim full_name: Quatmann, Tim last_name: Quatmann - first_name: Maximilian full_name: Schäffeler, Maximilian last_name: Schäffeler - first_name: Maximilian full_name: Weininger, Maximilian id: 02ab0197-cc70-11ed-ab61-918e71f56881 last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler - first_name: Daniel full_name: Zilken, Daniel id: d8ebc24a-3f98-11f0-9044-8296d4f39ab3 last_name: Zilken citation: ama: 'Chatterjee K, Quatmann T, Schäffeler M, Weininger M, Winkler T, Zilken D. Artifact: Fixed point certificates for reachability and expected rewards in MDPs. 2025. doi:10.5281/ZENODO.14626585' apa: 'Chatterjee, K., Quatmann, T., Schäffeler, M., Weininger, M., Winkler, T., & Zilken, D. (2025). Artifact: Fixed point certificates for reachability and expected rewards in MDPs. Zenodo. https://doi.org/10.5281/ZENODO.14626585' chicago: 'Chatterjee, Krishnendu, Tim Quatmann, Maximilian Schäffeler, Maximilian Weininger, Tobias Winkler, and Daniel Zilken. “Artifact: Fixed Point Certificates for Reachability and Expected Rewards in MDPs.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.14626585.' ieee: 'K. Chatterjee, T. Quatmann, M. Schäffeler, M. Weininger, T. Winkler, and D. Zilken, “Artifact: Fixed point certificates for reachability and expected rewards in MDPs.” Zenodo, 2025.' ista: 'Chatterjee K, Quatmann T, Schäffeler M, Weininger M, Winkler T, Zilken D. 2025. Artifact: Fixed point certificates for reachability and expected rewards in MDPs, Zenodo, 10.5281/ZENODO.14626585.' mla: 'Chatterjee, Krishnendu, et al. Artifact: Fixed Point Certificates for Reachability and Expected Rewards in MDPs. Zenodo, 2025, doi:10.5281/ZENODO.14626585.' short: K. Chatterjee, T. Quatmann, M. Schäffeler, M. Weininger, T. Winkler, D. Zilken, (2025). date_created: 2025-06-02T10:13:24Z date_published: 2025-01-09T00:00:00Z date_updated: 2025-06-02T10:55:35Z day: '09' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.14626585 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.14626585 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '19743' relation: used_in_publication status: public status: public title: 'Artifact: Fixed point certificates for reachability and expected rewards in MDPs' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19796' abstract: - lang: eng text: "Motivation: Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram (SD) describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. Efficient computational tools for studying SDs are essential for the understanding of Boolean attractor landscapes and connecting them to their biological functions.\r\nResults: We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist’s Boolean attractor landscape mapper, biobalm. We compare biobalm to similar tools and find a substantial performance increase in SD construction, attractor identification, and attractor control. We perform the most comprehensive comparative analysis to date of the SD structure in experimentally-validated Boolean models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small SDs, indicating simple decision structures. In contrast, nonrandom models from the literature are enriched in extremely large SDs, indicating an abundance of decision points and suggesting the presence of complex Waddington landscapes in nature.\r\nAvailability and implementation: The tool biobalm is available online at https://github.com/jcrozum/biobalm. Further data, scripts for testing, analysis, and figure generation are available online at https://github.com/jcrozum/biobalm-analysis and in the reproducibility artefact at https://doi.org/10.5281/zenodo.13854760." acknowledgement: V.-G.T. was supported by Institut Carnot STAR, Marseille, France. K.H.P. was supported by NSF grant MCB1715826 to Réka Albert. S.P. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. J.C.R. was supported by internal departmental funds provided by Luis M. Rocha. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the article. article_number: btaf280 article_processing_charge: Yes article_type: original author: - first_name: Van Giang full_name: Trinh, Van Giang last_name: Trinh - first_name: Kyu Hyong full_name: Park, Kyu Hyong last_name: Park - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: Jordan C. full_name: Rozum, Jordan C. last_name: Rozum citation: ama: Trinh VG, Park KH, Pastva S, Rozum JC. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 2025;41(5). doi:10.1093/bioinformatics/btaf280 apa: Trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. C. (2025). Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaf280 chicago: Trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan C. Rozum. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics. Oxford University Press, 2025. https://doi.org/10.1093/bioinformatics/btaf280. ieee: V. G. Trinh, K. H. Park, S. Pastva, and J. C. Rozum, “Mapping the attractor landscape of Boolean networks with biobalm,” Bioinformatics, vol. 41, no. 5. Oxford University Press, 2025. ista: Trinh VG, Park KH, Pastva S, Rozum JC. 2025. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 41(5), btaf280. mla: Trinh, Van Giang, et al. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics, vol. 41, no. 5, btaf280, Oxford University Press, 2025, doi:10.1093/bioinformatics/btaf280. short: V.G. Trinh, K.H. Park, S. Pastva, J.C. Rozum, Bioinformatics 41 (2025). corr_author: '1' date_created: 2025-06-08T22:01:22Z date_published: 2025-05-01T00:00:00Z date_updated: 2025-09-30T12:46:33Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1093/bioinformatics/btaf280 ec_funded: 1 external_id: isi: - '001493400600001' pmid: - '40327535' file: - access_level: open_access checksum: fa9d68aa0f5ce37598a623c9be936f09 content_type: application/pdf creator: dernst date_created: 2025-06-10T07:07:45Z date_updated: 2025-06-10T07:07:45Z file_id: '19801' file_name: 2025_Bioinformatics_Trinh.pdf file_size: 2695801 relation: main_file success: 1 file_date_updated: 2025-06-10T07:07:45Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/jcrozum/biobalm record: - id: '19800' relation: research_data status: public scopus_import: '1' status: public title: Mapping the attractor landscape of Boolean networks with biobalm 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: 41 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '20032' abstract: - lang: eng text: We propose Scalable Mechanistic Neural Network (S-MNN), an enhanced neural network framework designed for scientific machine learning applications involving long temporal sequences. By reformulating the original Mechanistic Neural Network (MNN) (Pervez et al., 2024), we reduce the computational time and space complexities from cubic and quadratic with respect to the sequence length, respectively, to linear. This significant improvement enables efficient modeling of long-term dynamics without sacrificing accuracy or interpretability. Extensive experiments demonstrate that S-MNN matches the original MNN in precision while substantially reducing computational resources. Consequently, S-MNN can drop-in replace the original MNN in applications, providing a practical and efficient tool for integrating mechanistic bottlenecks into neural network models of complex dynamical systems. Source code is available at https://github.com/IST-DASLab/ScalableMNN. article_processing_charge: No arxiv: 1 author: - first_name: Jiale full_name: Chen, Jiale id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785 last_name: Chen orcid: 0000-0001-5337-5875 - first_name: Dingling full_name: Yao, Dingling id: d3e02e50-48a8-11ee-8f62-c108061797fa last_name: Yao - first_name: Adeel A full_name: Pervez, Adeel A id: fca6d90c-d47f-11ee-bc87-93ff51604981 last_name: Pervez - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. Scalable mechanistic neural networks. In: 13th International Conference on Learning Representations. ICLR; 2025:63716-63737.' apa: 'Chen, J., Yao, D., Pervez, A. A., Alistarh, D.-A., & Locatello, F. (2025). Scalable mechanistic neural networks. In 13th International Conference on Learning Representations (pp. 63716–63737). Singapore, Singapore: ICLR.' chicago: Chen, Jiale, Dingling Yao, Adeel A Pervez, Dan-Adrian Alistarh, and Francesco Locatello. “Scalable Mechanistic Neural Networks.” In 13th International Conference on Learning Representations, 63716–37. ICLR, 2025. ieee: J. Chen, D. Yao, A. A. Pervez, D.-A. Alistarh, and F. Locatello, “Scalable mechanistic neural networks,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 63716–63737. ista: 'Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. 2025. Scalable mechanistic neural networks. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 63716–63737.' mla: Chen, Jiale, et al. “Scalable Mechanistic Neural Networks.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–37. short: J. Chen, D. Yao, A.A. Pervez, D.-A. Alistarh, F. Locatello, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–63737. conference: end_date: 2025-04-28 location: Singapore, Singapore name: 'ICLR: International Conference on Learning Representations' start_date: 2025-04-24 corr_author: '1' date_created: 2025-07-20T22:02:01Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-08-04T08:03:11Z day: '01' ddc: - '000' department: - _id: DaAl - _id: FrLo external_id: arxiv: - '2410.06074' file: - access_level: open_access checksum: 64cfdb12ae3e4e8ba57b1403e1066776 content_type: application/pdf creator: dernst date_created: 2025-07-22T07:58:22Z date_updated: 2025-07-22T07:58:22Z file_id: '20065' file_name: 2025_ICLR_Chen.pdf file_size: 732745 relation: main_file success: 1 file_date_updated: 2025-07-22T07:58:22Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 63716-63737 publication: 13th International Conference on Learning Representations publication_identifier: isbn: - '9798331320850' publication_status: published publisher: ICLR quality_controlled: '1' related_material: link: - relation: software url: https://github.com/IST-DASLab/ScalableMNN scopus_import: '1' status: public title: Scalable mechanistic neural networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20546' abstract: - lang: eng text: Rocky debris covers around 7.3 % of the global glacier area, influencing ice melt rates and the surface mass balance of glaciers, making the dynamics and hydrology of debris-covered glaciers distinct from those of clean-ice glaciers. Accurate representation of debris in models is challenging, as measurements of the physical properties and thickness of the supraglacial debris layer are scarce. Here, we compile a database of measured and reported bulk physical properties and layer thicknesses of supraglacial debris that we call the supraglacial Debris Database (DebDaB) and that is open to community submissions. The majority of the database (90 %) is compiled from 172 sources in the literature, and the remaining 10 % was previously unpublished. DebDaB contains 8741 data entries for supraglacial debris layer thickness, of which 1770 entries also include sub-debris ablation rates, 179 thermal conductivity of debris, 160 aerodynamic surface roughness length, 79 debris albedo, 59 debris emissivity, and 37 debris porosity. The data are distributed over 84 glaciers in 13 regions in the Global Terrestrial Network for Glaciers. We show regional differences in the distribution of debris thickness measurements in DebDaB and fit simplified Østrem curves to 19 glaciers with sufficient debris thickness and ablation data. The data in DebDaB can be used for energy balance, melt, and surface mass balance studies by incorporating site-specific debris properties or for evaluation of remote sensing estimates of debris thickness and surface roughness. They can also help future field campaigns on debris-covered glaciers by identifying observation gaps. DebDaB's uneven spatial coverage points to sampling biases in community efforts to observe debris-covered glaciers, with some regions (e.g. central Europe and South Asia) well-sampled but others having gaps with prevalent debris (e.g. the Andes and Alaska). Debris thickness measurements are mostly concentrated at lower elevations, leaving higher-elevation debris-covered areas undersampled and suggesting that our knowledge of debris properties might not be representative of all elevations. The aims of DebDaB, as an openly available dataset, are to evolve over time, to be updated, and to add to community submissions as new data on supraglacial properties become available. The data described in this paper can be accessed from Zenodo at https://doi.org/10.5281/zenodo.14224835 (Groeneveld et al., 2025). acknowledgement: "This work was supported by SNF project RENOIR (“Resolving the thickness of debris on Earth’s glaciers and its rate of change”; grant no. 204322). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and\r\ninnovation programme (grant no. 772751; RAVEN: “Rapid mass losses of debris covered glaciers in High Mountain Asia”). The authors acknowledge DCGWG of IACS for setting the stage and bringing together the debris-covered glacier community to focus on broader needs transcending a specific research topic and for starting the Zenodo community on debris-covered glaciers, where this database is hosted. The authors thank Achim A. Beylich (topical editor), Ken\r\nMankoff (chief editor), Morgan Jones (reviewer), and an anonymous reviewer for their constructive feedback, comments, and discussions on the database and paper." article_processing_charge: Yes article_type: original author: - first_name: Adrià full_name: Fontrodona-Bach, Adrià id: f06891fd-9f42-11ee-8632-a20971c43046 last_name: Fontrodona-Bach - first_name: Lars full_name: Groeneveld, Lars last_name: Groeneveld - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw orcid: 0000-0001-7640-6152 - first_name: Juan Vicente full_name: Melo Velasco, Juan Vicente id: 2611dec0-b9c6-11ed-9bea-a81c2b17a549 last_name: Melo Velasco - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Fontrodona-Bach A, Groeneveld L, Miles E, et al. DebDaB: A database of supraglacial debris  thickness and physical properties. Earth System Science Data. 2025;17(8):4213-4234. doi:10.5194/essd-17-4213-2025' apa: 'Fontrodona-Bach, A., Groeneveld, L., Miles, E., McCarthy, M., Shaw, T., Melo Velasco, J. V., & Pellicciotti, F. (2025). DebDaB: A database of supraglacial debris  thickness and physical properties. Earth System Science Data. Copernicus Publications. https://doi.org/10.5194/essd-17-4213-2025' chicago: 'Fontrodona-Bach, Adrià, Lars Groeneveld, Evan Miles, Michael McCarthy, Thomas Shaw, Juan Vicente Melo Velasco, and Francesca Pellicciotti. “DebDaB: A Database of Supraglacial Debris  Thickness and Physical Properties.” Earth System Science Data. Copernicus Publications, 2025. https://doi.org/10.5194/essd-17-4213-2025.' ieee: 'A. Fontrodona-Bach et al., “DebDaB: A database of supraglacial debris  thickness and physical properties,” Earth System Science Data, vol. 17, no. 8. Copernicus Publications, pp. 4213–4234, 2025.' ista: 'Fontrodona-Bach A, Groeneveld L, Miles E, McCarthy M, Shaw T, Melo Velasco JV, Pellicciotti F. 2025. DebDaB: A database of supraglacial debris  thickness and physical properties. Earth System Science Data. 17(8), 4213–4234.' mla: 'Fontrodona-Bach, Adrià, et al. “DebDaB: A Database of Supraglacial Debris  Thickness and Physical Properties.” Earth System Science Data, vol. 17, no. 8, Copernicus Publications, 2025, pp. 4213–34, doi:10.5194/essd-17-4213-2025.' short: A. Fontrodona-Bach, L. Groeneveld, E. Miles, M. McCarthy, T. Shaw, J.V. Melo Velasco, F. Pellicciotti, Earth System Science Data 17 (2025) 4213–4234. corr_author: '1' date_created: 2025-10-27T08:21:22Z date_published: 2025-08-29T00:00:00Z date_updated: 2025-12-01T15:05:58Z day: '29' ddc: - '550' department: - _id: FrPe doi: 10.5194/essd-17-4213-2025 external_id: isi: - '001560847000001' file: - access_level: open_access checksum: f77ebb9825f374134a89e0e6311fe188 content_type: application/pdf creator: dernst date_created: 2025-10-27T08:38:40Z date_updated: 2025-10-27T08:38:40Z file_id: '20548' file_name: 2025_EarthSystemScienceData_FontrodonaBach.pdf file_size: 3842196 relation: main_file success: 1 file_date_updated: 2025-10-27T08:38:40Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 4213-4234 publication: Earth System Science Data publication_identifier: issn: - 1866-3516 publication_status: published publisher: Copernicus Publications quality_controlled: '1' related_material: record: - id: '20547' relation: research_data status: public scopus_import: '1' status: public title: 'DebDaB: A database of supraglacial debris thickness and physical properties' 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: 17 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '17240' abstract: - lang: eng text: We prove an upper bound on the energy density of the dilute spin-\(\frac {1}{2}\) Fermi gas capturing the leading correction to the kinetic energy\(8\pi a\rho _\uparrow\rho _\downarrow\) with an error of size smaller than\(a\rho^{2}(a^ 3\rho)^{1/3-\varepsilon}\) for any\(\varepsilon> 0\), where a denotes the scattering length of the interaction. The result is valid for a large class of interactions including interactions with a hard core. A central ingredient in the proof is a rigorous version of a fermionic cluster expansion adapted from the formal expansion of Gaudin et al. (Nucl Phys A 176(2):237–260, 1971. https://doi.org/10.1016/0375-9474(71)90267-3). acknowledgement: "Open access funding provided by Institute of Science and Technology (IST Austria).\r\nWe thank Alessandro Giuliani and Robert Seiringer for helpful discussions and Robert Seiringer for his comments on the manuscript. Financial support by the Austrian Science Fund (FWF) through Grant https://doi.org/10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Lauritsen AB. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. 2025;26:203-243. doi:10.1007/s00023-024-01450-1 apa: Lauritsen, A. B. (2025). Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-024-01450-1 chicago: Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” Annales Henri Poincare. Springer Nature, 2025. https://doi.org/10.1007/s00023-024-01450-1. ieee: A. B. Lauritsen, “Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion,” Annales Henri Poincare, vol. 26. Springer Nature, pp. 203–243, 2025. ista: Lauritsen AB. 2025. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. 26, 203–243. mla: Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” Annales Henri Poincare, vol. 26, Springer Nature, 2025, pp. 203–43, doi:10.1007/s00023-024-01450-1. short: A.B. Lauritsen, Annales Henri Poincare 26 (2025) 203–243. corr_author: '1' date_created: 2024-07-14T22:01:12Z date_published: 2025-01-01T00:00:00Z date_updated: 2026-04-07T13:01:40Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00023-024-01450-1 external_id: isi: - '001261197700002' pmid: - '39926012' file: - access_level: open_access checksum: 01b6572f55f721e97498522c85072ed2 content_type: application/pdf creator: dernst date_created: 2025-08-05T11:42:27Z date_updated: 2025-08-05T11:42:27Z file_id: '20125' file_name: 2025_AnnalesHenriPoincare_Lauritsen.pdf file_size: 797241 relation: main_file success: 1 file_date_updated: 2025-08-05T11:42:27Z has_accepted_license: '1' intvolume: ' 26' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 203-243 pmid: 1 project: - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '18135' relation: dissertation_contains status: public scopus_import: '1' status: public title: Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion 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: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '20850' abstract: - lang: eng text: We provide an estimate for the number of nontrivial integer points on the Pellian surface t^2 - du^2 = 1 in a bounded region. We give a lower bound on the size of fundamental solutions for almost all d in a certain class, based on a recent conjecture of Browning and Wilsch about integer points on log K3 surfaces. We also obtain an upper bound on the average of class number in this class, assuming the same conjecture. - lang: fre text: "Nous donnons une estimation du nombre de points entiers non triviaux sur la surface pellienne \r\nt^2 - du^2 = 1 dans une région bornée. Nous établissons une borne inférieure pour la taille des solutions fondamentales pour presque tout d appartenant à une certaine classe, en nous fondant sur une conjecture récente de Browning et Wilsch concernant les points entiers sur les surfaces log K3. Nous obtenons également une borne supérieure pour la moyenne du nombre de classes dans cette classe, sous la même hypothèse conjecturale." acknowledgement: The author would like to thank his supervisor Tim Browning for suggesting this project and many helpful conversations and useful comments. Moreover, he is grateful to Jakob Glas, Damaris Schindler, Igor Shparlinski, Matteo Verzobio, Victor Wang, Florian Wilsch and Shuntaro Yamagishi for taking their time to answer his questions and their valuable suggestions. article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Yijie full_name: Diao, Yijie id: 7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b last_name: Diao orcid: 0000-0002-4989-5330 citation: ama: Diao Y. Class numbers and integer points on some Pellian surfaces. Journal de theorie des nombres de Bordeaux. 2025;37(3):973-988. doi:10.5802/jtnb.1348 apa: Diao, Y. (2025). Class numbers and integer points on some Pellian surfaces. Journal de Theorie Des Nombres de Bordeaux. Université de Bordeaux. https://doi.org/10.5802/jtnb.1348 chicago: Diao, Yijie. “Class Numbers and Integer Points on Some Pellian Surfaces.” Journal de Theorie Des Nombres de Bordeaux. Université de Bordeaux, 2025. https://doi.org/10.5802/jtnb.1348. ieee: Y. Diao, “Class numbers and integer points on some Pellian surfaces,” Journal de theorie des nombres de Bordeaux, vol. 37, no. 3. Université de Bordeaux, pp. 973–988, 2025. ista: Diao Y. 2025. Class numbers and integer points on some Pellian surfaces. Journal de theorie des nombres de Bordeaux. 37(3), 973–988. mla: Diao, Yijie. “Class Numbers and Integer Points on Some Pellian Surfaces.” Journal de Theorie Des Nombres de Bordeaux, vol. 37, no. 3, Université de Bordeaux, 2025, pp. 973–88, doi:10.5802/jtnb.1348. short: Y. Diao, Journal de Theorie Des Nombres de Bordeaux 37 (2025) 973–988. corr_author: '1' das_tickbox: '0' date_created: 2025-12-21T23:01:35Z date_published: 2025-11-27T00:00:00Z date_updated: 2026-07-16T08:45:12Z day: '27' ddc: - '510' department: - _id: TiBr doi: 10.5802/jtnb.1348 external_id: arxiv: - '2408.03774' file: - access_level: open_access checksum: 67aa0afbc0b5bcbff5341f4d25e6ba20 content_type: application/pdf creator: dernst date_created: 2025-12-29T10:05:22Z date_updated: 2025-12-29T10:05:22Z file_id: '20861' file_name: 2025_JTNB_Diao.pdf file_size: 766196 relation: main_file success: 1 file_date_updated: 2025-12-29T10:05:22Z has_accepted_license: '1' intvolume: ' 37' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '11' oa: 1 oa_version: Published Version page: 973-988 publication: Journal de theorie des nombres de Bordeaux publication_identifier: eissn: - 2118-8572 issn: - 1246-7405 publication_status: published publisher: Université de Bordeaux quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Class numbers and integer points on some Pellian surfaces tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 37 year: '2025' ... --- OA_place: repository OA_type: green _id: '21068' abstract: - lang: eng text: "Causal reasoning and discovery, two fundamental tasks of causal analysis,\r\noften face challenges in applications due to the complexity, noisiness, and highdimensionality of real-world data. Despite recent progress in identifying latent\r\ncausal structures using causal representation learning (CRL), what makes learned\r\nrepresentations useful for causal downstream tasks and how to evaluate them are\r\nstill not well understood. In this paper, we reinterpret CRL using a measurement\r\nmodel framework, where the learned representations are viewed as proxy measurements of the latent causal variables. Our approach clarifies the conditions under\r\nwhich learned representations support downstream causal reasoning and provides\r\na principled basis for quantitatively assessing the quality of representations using\r\na new Test-based Measurement EXclusivity (T-MEX) score. We validate T-MEX\r\nacross diverse causal inference scenarios, including numerical simulations and\r\nreal-world ecological video analysis, demonstrating that the proposed framework\r\nand corresponding score effectively assess the identification of learned representations and their usefulness for causal downstream tasks. Reproducible code can\r\nbe found at https://github.com/shimenghuang/a-measurement-perspective-of-crl." acknowledgement: "This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/COE12. For open access purposes, the author has applied a CC BY public copyright license to any accepted manuscript version arising from this submission.\r\n" alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Dingling full_name: Yao, Dingling id: d3e02e50-48a8-11ee-8f62-c108061797fa last_name: Yao - first_name: Shimeng full_name: Huang, Shimeng id: 989c2a06-fb4e-11ef-a992-ab766442255b last_name: Huang orcid: 0000-0001-6919-821X - first_name: Riccardo full_name: Cadei, Riccardo id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b last_name: Cadei - first_name: Kun full_name: Zhang, Kun last_name: Zhang - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Yao D, Huang S, Cadei R, Zhang K, Locatello F. The third pillar of causal analysis? A measurement perspective on causal representations. In: 39th Annual Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025.' apa: 'Yao, D., Huang, S., Cadei, R., Zhang, K., & Locatello, F. (2025). The third pillar of causal analysis? A measurement perspective on causal representations. In 39th Annual Conference on Neural Information Processing Systems (Vol. 38). San Diego, CA, United States: Neural Information Processing Systems Foundation.' chicago: Yao, Dingling, Shimeng Huang, Riccardo Cadei, Kun Zhang, and Francesco Locatello. “The Third Pillar of Causal Analysis? A Measurement Perspective on Causal Representations.” In 39th Annual Conference on Neural Information Processing Systems, Vol. 38. Neural Information Processing Systems Foundation, 2025. ieee: D. Yao, S. Huang, R. Cadei, K. Zhang, and F. Locatello, “The third pillar of causal analysis? A measurement perspective on causal representations,” in 39th Annual Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38. ista: 'Yao D, Huang S, Cadei R, Zhang K, Locatello F. 2025. The third pillar of causal analysis? A measurement perspective on causal representations. 39th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38.' mla: Yao, Dingling, et al. “The Third Pillar of Causal Analysis? A Measurement Perspective on Causal Representations.” 39th Annual Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025. short: D. Yao, S. Huang, R. Cadei, K. Zhang, F. Locatello, in:, 39th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025. conference: end_date: 2025-12-07 location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2025-12-02 corr_author: '1' das_tickbox: '1' date_created: 2026-01-29T14:24:56Z date_published: 2025-12-15T00:00:00Z date_updated: 2026-07-28T07:14:27Z day: '15' ddc: - '000' department: - _id: FrLo external_id: arxiv: - '2505.17708' has_accepted_license: '1' intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2505.17708 month: '12' oa: 1 oa_version: Preprint publication: 39th Annual Conference on Neural Information Processing Systems publication_identifier: issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' related_material: link: - relation: software url: https://github.com/shimenghuang/a-measurement-perspective-of-crl status: public title: The third pillar of causal analysis? A measurement perspective on causal representations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_type: closed access _id: '20704' abstract: - lang: eng text: Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES. acknowledged_ssus: - _id: ScienComp acknowledgement: P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai. article_processing_charge: No article_type: original author: - first_name: Ping full_name: Tuo, Ping id: 6e5644c0-c180-11ed-a2da-facc4c9f4f09 last_name: Tuo - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Jiale full_name: Chen, Jiale id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785 last_name: Chen orcid: 0000-0001-5337-5875 - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248 apa: Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248 chicago: Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248. ieee: P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” Journal of Chemical Theory and Computation, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025. ista: Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435. mla: Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248. short: P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435. corr_author: '1' das_tickbox: '0' date_created: 2025-11-30T23:02:06Z date_published: 2025-10-31T00:00:00Z date_updated: 2026-08-07T10:29:06Z day: '31' department: - _id: BiCh - _id: DaAl doi: 10.1021/acs.jctc.5c01248 ec_funded: 1 external_id: isi: - '001605927900001' pmid: - '41172130' intvolume: ' 21' isi: 1 issue: '22' language: - iso: eng month: '10' oa_version: None page: 11427-11435 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/tuoping/alchemicalFES researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Scalable multitemperature free energy sampling of classical Ising spin states type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '22568' abstract: - lang: eng text: "The recent surge in reservoir construction has increased global surface water storage, with Mainland\r\nSoutheast Asia (MSEA) being a significant hotspot. Such infrastructural evolution demands updates in water\r\nmanagement strategies and hydrological models. However, information on actual reservoir storage is hard to\r\nacquire, especially for transboundary river basins. To date, no high-resolution spatiotemporal dataset on absolute\r\nstorage time series is available for reservoirs in MSEA. To address this gap, we present (1) a comprehensive openaccess database of absolute storage time series (sub-monthly) for 186 reservoirs (larger than 0.1 km3) in MSEA\r\nspanning the period 1985–2023 and (2) an analysis of the reservoir storage dynamics. This dataset is derived\r\nfrom remote sensing observations, integrating satellite-based water surface area extraction from high-resolution\r\n(30 m) images and area–elevation–storage (A–E–S) relationships to estimate reservoir level and storage dynamics. The MSEA database includes static (area–elevation–storage curves, water frequency, and reservoir extent)\r\nand dynamic (area, water level, and absolute storage time series) components for each reservoir. The 186 reservoirs collectively store around 175 km3 of water, with a minimum of 140 km3 and a maximum of 210 km3. They\r\ncover an average area of 8700 km2, ranging from a minimum of 6500 km2 to a maximum of 10 000 km2. We show that the combined average reservoir storage increased from 70 to 160 km3 (+130 %) from 2008 to 2017, primarily contributed by reservoirs in the Irrawaddy, Red, Upper Mekong, and Lower Mekong basins. Our in situ validation provides a good match between estimated storage and in situ observations, with 50 % of the validation sites (10 out of 20) showing an R2 > 0.7 and an average nRMSE < 14 %. The indirect validation (based on altimetry-converted storage) shows even better results, with an R2 > 0.7 and an average nRMSE < 12 % for 70 % (14 out of 20) of the reservoirs. Furthermore, the analysis of the 2019–2020 drought event in the MSEA region reveals that nearly 30 %–40 % of the region experienced more than 5 months of drought, with the most significant impact on reservoirs in Cambodia and Thailand. As a result, storage departures ranged by up to −40 % in some reservoirs, highlighting significant impacts on water availability. Overall, this analysis demonstrates the potential of the inferred storage time series for assessing real-life water-related problems in Mainland Southeast Asia, with the possibility of applying the method to estimate reservoir storage time series in other parts of the world. The reservoir storage database in Mainland Southeast Asia (MSEA-Res database) and the associated Python code are publicly available on Zenodo at https://doi.org/10.5281/zenodo.14844580 (Mahto et al., 2025)." article_processing_charge: No article_type: original author: - first_name: Shanti Shwarup full_name: Mahto, Shanti Shwarup last_name: Mahto - first_name: Simone full_name: Fatichi, Simone id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6 last_name: Fatichi - first_name: Stefano full_name: Galelli, Stefano last_name: Galelli citation: ama: Mahto SS, Fatichi S, Galelli S. A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. 2025;17(6):2693-2712. doi:10.5194/essd-17-2693-2025 apa: Mahto, S. S., Fatichi, S., & Galelli, S. (2025). A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. Copernicus Publications. https://doi.org/10.5194/essd-17-2693-2025 chicago: Mahto, Shanti Shwarup, Simone Fatichi, and Stefano Galelli. “A 1985–2023 Time Series Dataset of Absolute Reservoir Storage in Mainland Southeast Asia (MSEA-Res).” Earth System Science Data. Copernicus Publications, 2025. https://doi.org/10.5194/essd-17-2693-2025. ieee: S. S. Mahto, S. Fatichi, and S. Galelli, “A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res),” Earth System Science Data, vol. 17, no. 6. Copernicus Publications, pp. 2693–2712, 2025. ista: Mahto SS, Fatichi S, Galelli S. 2025. A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. 17(6), 2693–2712. mla: Mahto, Shanti Shwarup, et al. “A 1985–2023 Time Series Dataset of Absolute Reservoir Storage in Mainland Southeast Asia (MSEA-Res).” Earth System Science Data, vol. 17, no. 6, Copernicus Publications, 2025, pp. 2693–712, doi:10.5194/essd-17-2693-2025. short: S.S. Mahto, S. Fatichi, S. Galelli, Earth System Science Data 17 (2025) 2693–2712. das_tickbox: '1' date_created: 2026-07-27T12:30:24Z date_published: 2025-06-17T00:00:00Z date_updated: 2026-08-07T10:54:05Z day: '17' doi: 10.5194/essd-17-2693-2025 extern: '1' intvolume: ' 17' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5194/essd-17-2693-2025 month: '06' oa: 1 oa_version: Published Version page: 2693-2712 publication: Earth System Science Data publication_identifier: eissn: - 1866-3516 issn: - 1866-3508 publication_status: published publisher: Copernicus Publications quality_controlled: '1' scopus_import: '1' status: public title: A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res) 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: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 17 year: '2025' ...