[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Scalable multitemperature free energy sampling of classical Ising spin states","researchdata_availability":"no","day":"31","department":[{"_id":"BiCh"},{"_id":"DaAl"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"doi":"10.1021/acs.jctc.5c01248","isi":1,"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.","publisher":"American Chemical Society","das_tickbox":"0","date_published":"2025-10-31T00:00:00Z","_id":"20704","quality_controlled":"1","year":"2025","publication_status":"published","related_material":{"link":[{"url":"https://github.com/tuoping/alchemicalFES","relation":"software"}]},"issue":"22","volume":21,"month":"10","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"id":"6e5644c0-c180-11ed-a2da-facc4c9f4f09","full_name":"Tuo, Ping","last_name":"Tuo","first_name":"Ping"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","full_name":"Zeng, Zezhu","last_name":"Zeng","first_name":"Zezhu","orcid":"0000-0001-5126-4928"},{"id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","full_name":"Chen, Jiale","last_name":"Chen","first_name":"Jiale","orcid":"0000-0001-5337-5875"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"}],"pmid":1,"page":"11427-11435","intvolume":" 21","date_updated":"2026-08-07T10:29:06Z","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"OA_type":"closed access","date_created":"2025-11-30T23:02:06Z","publication":"Journal of Chemical Theory and Computation","oa_version":"None","scopus_import":"1","corr_author":"1","type":"journal_article","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."}],"external_id":{"pmid":["41172130"],"isi":["001605927900001"]},"status":"public","supplementarymaterial":"no","citation":{"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.","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","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","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.","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.","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."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}]},{"author":[{"first_name":"Jordi","last_name":"Buckley Paules","full_name":"Buckley Paules, Jordi"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone","last_name":"Fatichi","first_name":"Simone"},{"first_name":"Bonnie","last_name":"Warring","full_name":"Warring, Bonnie"},{"full_name":"Paschalis, Athanasios","last_name":"Paschalis","first_name":"Athanasios"}],"page":"1287-1305","year":"2025","publication_status":"published","issue":"4","volume":18,"month":"03","date_created":"2026-07-27T12:30:24Z","publication":"Geoscientific Model Development","scopus_import":"1","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/gmd-18-1287-2025"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Cropland cultivation is fundamental to food security and plays a crucial role in the global water, energy, and carbon cycles. However, our understanding of how climate change will impact cropland functions is still limited. This knowledge gap is partly due to the simplifications made in terrestrial biosphere models (TBMs), which often overlook essential agricultural management practices such as irrigation and fertilizer application and simplify critical physiological crop processes.\r\nHere, we demonstrate how, with minor, parsimonious enhancements to the TBM T&C, it is possible to accurately represent a complex cropland system. Our modified model, T&C-CROP, incorporates realistic agricultural management practices, including complex crop rotations and irrigation and fertilization regimes, along with their effects on soil biogeochemical cycling. We successfully validate T&C-CROP across four distinct agricultural sites, encompassing diverse cropping systems such as multi-crop rotations, monoculture, and managed grassland.\r\nA comprehensive validation of T&C-CROP was conducted, encompassing water, energy, and carbon fluxes; leaf area index (LAI); and organ-specific yields. Our model effectively captured the heterogeneity in daily land surface energy balances across crop sites, achieving coefficients of determination of 0.77, 0.48, and 0.87 for observed versus simulated net radiation (Rn), sensible heat flux (H), and latent heat flux (LE), respectively. Seasonal, crop-specific gross primary production (GPP) was simulated with an average absolute bias of less than 10 %. Peak-season LAI was accurately represented, with an r2 of 0.67. Harvested yields (above-ground biomass, grain, and straw) were generally simulated within 10 %–20 % accuracy of observed values, although inter-annual variations in crop-specific growth were difficult to capture."}],"status":"public","article_type":"original","DOAJ_listed":"1","citation":{"chicago":"Buckley Paules, Jordi, Simone Fatichi, Bonnie Warring, and Athanasios Paschalis. “T&C-CROP: Representing Mechanistic Crop Growth with a Terrestrial Biosphere Model (T&C, v1.5) – Model Formulation and Validation.” Geoscientific Model Development. Copernicus Publications, 2025. https://doi.org/10.5194/gmd-18-1287-2025.","mla":"Buckley Paules, Jordi, et al. “T&C-CROP: Representing Mechanistic Crop Growth with a Terrestrial Biosphere Model (T&C, v1.5) – Model Formulation and Validation.” Geoscientific Model Development, vol. 18, no. 4, Copernicus Publications, 2025, pp. 1287–305, doi:10.5194/gmd-18-1287-2025.","short":"J. Buckley Paules, S. Fatichi, B. Warring, A. Paschalis, Geoscientific Model Development 18 (2025) 1287–1305.","apa":"Buckley Paules, J., Fatichi, S., Warring, B., & Paschalis, A. (2025). T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation. Geoscientific Model Development. Copernicus Publications. https://doi.org/10.5194/gmd-18-1287-2025","ieee":"J. Buckley Paules, S. Fatichi, B. Warring, and A. Paschalis, “T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation,” Geoscientific Model Development, vol. 18, no. 4. Copernicus Publications, pp. 1287–1305, 2025.","ama":"Buckley Paules J, Fatichi S, Warring B, Paschalis A. T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation. Geoscientific Model Development. 2025;18(4):1287-1305. doi:10.5194/gmd-18-1287-2025","ista":"Buckley Paules J, Fatichi S, Warring B, Paschalis A. 2025. T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation. Geoscientific Model Development. 18(4), 1287–1305."},"language":[{"iso":"eng"}],"intvolume":" 18","OA_place":"publisher","date_updated":"2026-08-07T10:31:51Z","OA_type":"gold","article_processing_charge":"No","publication_identifier":{"issn":["1991-959X"],"eissn":["1991-9603"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere model (T&C, v1.5) – model formulation and validation","day":"03","das_tickbox":"1","_id":"22525","date_published":"2025-03-03T00:00:00Z","quality_controlled":"1","extern":"1","doi":"10.5194/gmd-18-1287-2025","publisher":"Copernicus Publications"},{"language":[{"iso":"eng"}],"citation":{"apa":"Wang, Y., Meili, N., & Fatichi, S. (2025). Ecohydrological responses to solar radiation changes. Hydrology and Earth System Sciences. Copernicus Publications. https://doi.org/10.5194/hess-29-381-2025","ama":"Wang Y, Meili N, Fatichi S. Ecohydrological responses to solar radiation changes. Hydrology and Earth System Sciences. 2025;29(2):381-396. doi:10.5194/hess-29-381-2025","ista":"Wang Y, Meili N, Fatichi S. 2025. Ecohydrological responses to solar radiation changes. Hydrology and Earth System Sciences. 29(2), 381–396.","ieee":"Y. Wang, N. Meili, and S. Fatichi, “Ecohydrological responses to solar radiation changes,” Hydrology and Earth System Sciences, vol. 29, no. 2. Copernicus Publications, pp. 381–396, 2025.","mla":"Wang, Yiran, et al. “Ecohydrological Responses to Solar Radiation Changes.” Hydrology and Earth System Sciences, vol. 29, no. 2, Copernicus Publications, 2025, pp. 381–96, doi:10.5194/hess-29-381-2025.","short":"Y. Wang, N. Meili, S. Fatichi, Hydrology and Earth System Sciences 29 (2025) 381–396.","chicago":"Wang, Yiran, Naika Meili, and Simone Fatichi. “Ecohydrological Responses to Solar Radiation Changes.” Hydrology and Earth System Sciences. Copernicus Publications, 2025. https://doi.org/10.5194/hess-29-381-2025."},"DOAJ_listed":"1","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/hess-29-381-2025"}],"type":"journal_article","oa_version":"Published Version","date_created":"2026-07-27T12:30:24Z","publication":"Hydrology and Earth System Sciences","scopus_import":"1","status":"public","abstract":[{"text":"The implementation of future geoengineering projects to counteract global warming trends or more generally changes in aerosol loads alter solar radiation reaching the Earth's surface. These changes could have effects on ecohydrological systems with impacts which are still poorly quantified. Here, we compute how changes in solar radiation affect global and local near-surface meteorological variables by using CMIP6 model results. Using climate model outputs, we compute climate sensitivities to solar radiation alterations. These sensitivities are then applied to local observations and used to construct two sets of numerical experiments: the first focuses on solar radiation changes only, and the second systematically modifies precipitation, air temperature, specific humidity, and wind speed using the CMIP6-derived sensitivities to radiation changes, i.e., including its land–atmosphere feedback. We use those scenarios as input to a mechanistic ecohydrological model to quantify the local responses of the energy and water budgets as well as vegetation productivity spanning different biomes and climates.\r\nIn the absence of land–atmosphere feedback, changes in solar radiation tend to reflect mostly in sensible heat changes, with minor effects on the hydrological cycle, and vegetation productivity correlates linearly with changes in solar radiation. When land–atmosphere feedback is included, changes in latent heat and hydrological variables are much more pronounced, mostly because of the temperature and vapor pressure deficit changes associated with solar radiation changes. Vegetation productivity tends to have an asymmetric response with a considerable decrease in gross primary production to a radiation reduction not accompanied by a similar increase at higher radiation. These results provide important insights into how ecosystems could respond to potential future changes in shortwave radiation including solar geoengineering programs.","lang":"eng"}],"OA_type":"gold","intvolume":" 29","OA_place":"publisher","date_updated":"2026-08-07T10:42:02Z","page":"381-396","author":[{"first_name":"Yiran","last_name":"Wang","full_name":"Wang, Yiran"},{"full_name":"Meili, Naika","first_name":"Naika","last_name":"Meili"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone","first_name":"Simone","last_name":"Fatichi"}],"volume":29,"issue":"2","month":"01","year":"2025","publication_status":"published","date_published":"2025-01-21T00:00:00Z","_id":"22557","quality_controlled":"1","das_tickbox":"1","doi":"10.5194/hess-29-381-2025","publisher":"Copernicus Publications","extern":"1","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1607-7938"],"issn":["1027-5606"]},"day":"21","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Ecohydrological responses to solar radiation changes","oa":1},{"abstract":[{"lang":"eng","text":"Urbanization is projected to add 2.5 billion more urban residents by 2050. The resulting increases in impervious surfaces leads to altered hydrologic processes through greater runoff and reduced transpiration. Urban landscapes, characterized by heterogeneous land covers and infiltration rates, complicates the modeling of the urban water cycle. Existing models tend to focus on event-scale floods and thereby overlooking long-term hydrological alterations, as they often oversimplify hydrological processes such as soil moisture dynamics or evapotranspiration.\r\nAccurately projecting the long-term hydrological budget over cities is essential to better understand water resources availability for water sensitive urban design and to guide urban greening initiatives with the purpose of improving urban water management. Using Singapore —a densely populated tropical city-state committed to water harvesting— as a testbed, this study compares two modeling approaches to resolve the long-term urban hydrological budget. The Urban Tethys & Chloris (UT&C) model offers realistic representations of urban features, microclimate and hydrology, although it is computationally intensive. In contrast, the Tethys & Chloris (T&C) model, originally developed for natural environments, modified here to incorporate simplified urban features, is simpler and faster allowing fully distributed simulations.\r\nFindings suggest that while UT&C results may offer a more reliable representation at local scales, accounting for microclimatic feedback and two-dimensional urban geometries, both models yield similar hydrological budget insights when integrated at the city scale – at least in the wet climate of Singapore. Vegetation fraction emerges as the primary control on total evapotranspiration. T&C’s reduced computational demand, and native support for distributed hydrological modeling make it well-suited for city-wide simulations. The overall study underscores the complexities and feasibility of modeling long-term hydrological processes in urban environments."}],"status":"public","das_tickbox":"1","oa_version":"None","scopus_import":"1","publication":"Journal of Hydrology","date_created":"2026-07-27T12:30:24Z","type":"journal_article","article_type":"original","citation":{"chicago":"Lin Xu, Yexia, Naika Meili, and Simone Fatichi. “Long-Term Hydrological Budget over Urban Areas: Approaches and Challenges.” Journal of Hydrology. Elsevier, 2025. https://doi.org/10.1016/j.jhydrol.2025.134000.","mla":"Lin Xu, Yexia, et al. “Long-Term Hydrological Budget over Urban Areas: Approaches and Challenges.” Journal of Hydrology, vol. 662, Part B, 134000, Elsevier, 2025, doi:10.1016/j.jhydrol.2025.134000.","short":"Y. Lin Xu, N. Meili, S. Fatichi, Journal of Hydrology 662, Part B (2025).","apa":"Lin Xu, Y., Meili, N., & Fatichi, S. (2025). Long-term hydrological budget over urban areas: approaches and challenges. Journal of Hydrology. Elsevier. https://doi.org/10.1016/j.jhydrol.2025.134000","ista":"Lin Xu Y, Meili N, Fatichi S. 2025. Long-term hydrological budget over urban areas: approaches and challenges. Journal of Hydrology. 662, Part B, 134000.","ieee":"Y. Lin Xu, N. Meili, and S. Fatichi, “Long-term hydrological budget over urban areas: approaches and challenges,” Journal of Hydrology, vol. 662, Part B. Elsevier, 2025.","ama":"Lin Xu Y, Meili N, Fatichi S. Long-term hydrological budget over urban areas: approaches and challenges. Journal of Hydrology. 2025;662, Part B. doi:10.1016/j.jhydrol.2025.134000"},"language":[{"iso":"eng"}],"article_number":"134000","_id":"22539","quality_controlled":"1","date_published":"2025-12-01T00:00:00Z","date_updated":"2026-08-07T10:37:29Z","extern":"1","publisher":"Elsevier","OA_type":"closed access","doi":"10.1016/j.jhydrol.2025.134000","author":[{"first_name":"Yexia","last_name":"Lin Xu","full_name":"Lin Xu, Yexia"},{"first_name":"Naika","last_name":"Meili","full_name":"Meili, Naika"},{"last_name":"Fatichi","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone"}],"publication_identifier":{"issn":["0022-1694"],"eissn":["1879-2707"]},"article_processing_charge":"No","publication_status":"published","title":"Long-term hydrological budget over urban areas: approaches and challenges","year":"2025","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"12","day":"01","volume":"662, Part B"},{"article_type":"original","citation":{"chicago":"Chen, Liangzhi, Philipp Brun, Pascal Buri, Simone Fatichi, Arthur Gessler, Michael James McCarthy, Francesca Pellicciotti, Benjamin Stocker, and Dirk Nikolaus Karger. “Global Increase in the Occurrence and Impact of Multiyear Droughts.” Science. AAAS, 2025. https://doi.org/10.1126/science.ado4245.","short":"L. Chen, P. Brun, P. Buri, S. Fatichi, A. Gessler, M.J. McCarthy, F. Pellicciotti, B. Stocker, D.N. Karger, Science 387 (2025) 278–284.","mla":"Chen, Liangzhi, et al. “Global Increase in the Occurrence and Impact of Multiyear Droughts.” Science, vol. 387, no. 6731, AAAS, 2025, pp. 278–84, doi:10.1126/science.ado4245.","ama":"Chen L, Brun P, Buri P, et al. Global increase in the occurrence and impact of multiyear droughts. Science. 2025;387(6731):278-284. doi:10.1126/science.ado4245","ista":"Chen L, Brun P, Buri P, Fatichi S, Gessler A, McCarthy MJ, Pellicciotti F, Stocker B, Karger DN. 2025. Global increase in the occurrence and impact of multiyear droughts. Science. 387(6731), 278–284.","ieee":"L. Chen et al., “Global increase in the occurrence and impact of multiyear droughts,” Science, vol. 387, no. 6731. AAAS, pp. 278–284, 2025.","apa":"Chen, L., Brun, P., Buri, P., Fatichi, S., Gessler, A., McCarthy, M. J., … Karger, D. N. (2025). Global increase in the occurrence and impact of multiyear droughts. Science. AAAS. https://doi.org/10.1126/science.ado4245"},"language":[{"iso":"eng"}],"date_created":"2026-07-27T12:30:24Z","publication":"Science","scopus_import":"1","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Persistent multiyear drought (MYD) events pose a growing threat to nature and humans in a changing climate. We identified and inventoried global MYDs by detecting spatiotemporally contiguous climatic anomalies, showing that MYDs have become drier, hotter, and led to increasingly diminished vegetation greenness. The global terrestrial land affected by MYDs has increased at a rate of 49,279 ± 14,771 square kilometers per year from 1980 to 2018. Temperate grasslands have exhibited the greatest declines in vegetation greenness during MYDs, whereas boreal and tropical forests have had comparably minor responses. With MYDs becoming more common, this global quantitative inventory of the occurrence, severity, trend, and impact of MYDs provides an important benchmark for facilitating more effective and collaborative preparedness toward mitigation of and adaptation to such extreme events."}],"status":"public","OA_type":"closed access","intvolume":" 387","date_updated":"2026-08-07T10:47:08Z","page":"278-284","author":[{"full_name":"Chen, Liangzhi","last_name":"Chen","first_name":"Liangzhi"},{"full_name":"Brun, Philipp","last_name":"Brun","first_name":"Philipp"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"},{"full_name":"Gessler, Arthur","last_name":"Gessler","first_name":"Arthur"},{"full_name":"McCarthy, Michael James","last_name":"McCarthy","first_name":"Michael James"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca"},{"full_name":"Stocker, Benjamin","first_name":"Benjamin","last_name":"Stocker"},{"full_name":"Karger, Dirk Nikolaus","first_name":"Dirk Nikolaus","last_name":"Karger"}],"issue":"6731","volume":387,"month":"01","year":"2025","publication_status":"published","quality_controlled":"1","_id":"22562","date_published":"2025-01-17T00:00:00Z","das_tickbox":"1","doi":"10.1126/science.ado4245","publisher":"AAAS","extern":"1","article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"day":"17","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Global increase in the occurrence and impact of multiyear droughts"},{"extern":"1","doi":"10.5194/essd-17-2693-2025","publisher":"Copernicus Publications","das_tickbox":"1","date_published":"2025-06-17T00:00:00Z","_id":"22568","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res)","oa":1,"day":"17","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1866-3516"],"issn":["1866-3508"]},"OA_place":"publisher","intvolume":" 17","date_updated":"2026-08-07T10:54:05Z","OA_type":"gold","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/essd-17-2693-2025"}],"type":"journal_article","scopus_import":"1","oa_version":"Published Version","date_created":"2026-07-27T12:30:24Z","publication":"Earth System Science Data","status":"public","abstract":[{"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).","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"short":"S.S. Mahto, S. Fatichi, S. Galelli, Earth System Science Data 17 (2025) 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.","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","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.","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."},"DOAJ_listed":"1","article_type":"original","year":"2025","publication_status":"published","volume":17,"issue":"6","month":"06","author":[{"full_name":"Mahto, Shanti Shwarup","first_name":"Shanti Shwarup","last_name":"Mahto"},{"last_name":"Fatichi","first_name":"Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone"},{"last_name":"Galelli","first_name":"Stefano","full_name":"Galelli, Stefano"}],"page":"2693-2712"},{"date_updated":"2026-08-07T10:58:46Z","intvolume":" 135","OA_place":"publisher","OA_type":"hybrid","status":"public","abstract":[{"text":"Urban expansion alters landscape structure and hydrological processes, heightening pluvial flood risks in cities worldwide. This study integrates multi-temporal urban expansion data with the CAFlood cellular automata model to simulate rainfall events with multiple return periods (i.e., 1-in-10, 1-in-100, and 1-in-200 year return periods) across three different urban environments: Shenzhen (China), suburban Houston (United States), and Lausanne (Switzerland). To quantify how evolving urban morphology drives flood volume, we computed key landscape metrics describing impervious extent (percentage of impervious surface), green space shape complexity (Area-weighted Mean Shape Index), green space aggregation (Aggregation Index), and impervious edge complexity (Landscape Shape Index). Their effects on changes in flood volume were analysed with Generalised Additive Models stratified by levels of pre-expansion impervious cover. The results show that decreasing green space aggregation and impervious edge complexity are consistently significant indicators of increased flood volumes, particularly in areas with low pre-expansion impervious cover (<50 %). However, the influence of these two key morphological indicators decline as impervious coverage increases, with total imperviousness gradually becoming the dominant factor. Sensitivity experiments with synthetic urban fabrics confirm that maintaining compact, well-connected green spaces can limit the increase in flood volume even with when impervious surfaces expand equally. By explicitly linking the morphological changes in urban form to pluvial flood response across diverse climates and urbanisation context, this study moves beyond static approaches and provides actionable insights for planning flood-resilient urban growth.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.scs.2025.107018","open_access":"1"}],"type":"journal_article","oa_version":"Published Version","scopus_import":"1","date_created":"2026-07-27T12:30:24Z","publication":"Sustainable Cities and Society","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Zhu, Yue, Paolo Burlando, Ye Zhang, Dengkai Chi, Jing Wang, Yeshan Qiu, Matteo Bonatesta, et al. “The Influence of Urban Morphological Changes on Pluvial Flooding during Urban Expansion.” Sustainable Cities and Society. Elsevier, 2025. https://doi.org/10.1016/j.scs.2025.107018.","short":"Y. Zhu, P. Burlando, Y. Zhang, D. Chi, J. Wang, Y. Qiu, M. Bonatesta, W. Zou, C. Geiß, P.Y. Tan, S. Fatichi, Sustainable Cities and Society 135 (2025).","mla":"Zhu, Yue, et al. “The Influence of Urban Morphological Changes on Pluvial Flooding during Urban Expansion.” Sustainable Cities and Society, vol. 135, 107018, Elsevier, 2025, doi:10.1016/j.scs.2025.107018.","ista":"Zhu Y, Burlando P, Zhang Y, Chi D, Wang J, Qiu Y, Bonatesta M, Zou W, Geiß C, Tan PY, Fatichi S. 2025. The influence of urban morphological changes on pluvial flooding during urban expansion. Sustainable Cities and Society. 135, 107018.","ama":"Zhu Y, Burlando P, Zhang Y, et al. The influence of urban morphological changes on pluvial flooding during urban expansion. Sustainable Cities and Society. 2025;135. doi:10.1016/j.scs.2025.107018","ieee":"Y. Zhu et al., “The influence of urban morphological changes on pluvial flooding during urban expansion,” Sustainable Cities and Society, vol. 135. Elsevier, 2025.","apa":"Zhu, Y., Burlando, P., Zhang, Y., Chi, D., Wang, J., Qiu, Y., … Fatichi, S. (2025). The influence of urban morphological changes on pluvial flooding during urban expansion. Sustainable Cities and Society. Elsevier. https://doi.org/10.1016/j.scs.2025.107018"},"publication_status":"published","year":"2025","month":"12","volume":135,"author":[{"full_name":"Zhu, Yue","first_name":"Yue","last_name":"Zhu"},{"full_name":"Burlando, Paolo","first_name":"Paolo","last_name":"Burlando"},{"full_name":"Zhang, Ye","last_name":"Zhang","first_name":"Ye"},{"last_name":"Chi","first_name":"Dengkai","full_name":"Chi, Dengkai"},{"full_name":"Wang, Jing","first_name":"Jing","last_name":"Wang"},{"full_name":"Qiu, Yeshan","first_name":"Yeshan","last_name":"Qiu"},{"full_name":"Bonatesta, Matteo","last_name":"Bonatesta","first_name":"Matteo"},{"full_name":"Zou, Wenyue","last_name":"Zou","first_name":"Wenyue"},{"full_name":"Geiß, Christian","first_name":"Christian","last_name":"Geiß"},{"first_name":"Puay Yok","last_name":"Tan","full_name":"Tan, Puay Yok"},{"last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"}],"extern":"1","publisher":"Elsevier","doi":"10.1016/j.scs.2025.107018","das_tickbox":"1","article_number":"107018","quality_controlled":"1","_id":"22572","date_published":"2025-12-15T00:00:00Z","title":"The influence of urban morphological changes on pluvial flooding during urban expansion","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"15","keyword":["Urban morphology","Urban expansion","Pluvial flood","Flood resilience"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2210-6715"],"issn":["2210-6707"]},"article_processing_charge":"No"},{"das_tickbox":"1","quality_controlled":"1","_id":"22499","date_published":"2025-03-01T00:00:00Z","article_number":"e2024MS004590","extern":"1","doi":"10.1029/2024ms004590","publisher":"American Geophysical Union","article_processing_charge":"No","publication_identifier":{"eissn":["1942-2466"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates","day":"01","oa_version":"Published Version","date_created":"2026-07-27T12:30:24Z","scopus_import":"1","publication":"Journal of Advances in Modeling Earth Systems","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1029/2024MS004590","open_access":"1"}],"abstract":[{"text":"Increasing urban tree cover is a common strategy to lower urban temperatures and indirectly the building energy demand for air-conditioning (AC). However, urban vegetation leads to increasing humidity with potential negative effects on the AC dehumidification loads in hot-humid climates, an effect that has so far been unexplored. Here, we included a building energy model into the urban ecohydrological model Urban Tethys-Chloris (UT&C-BEM) to quantify the AC energy reduction effects of trees in seven hot cities with varying background humidity. A numerical experiment was performed simulating various urban densities and tree cover scenarios in the city-climates of Riyadh, Phoenix, Dubai, New Delhi, Singapore, Lagos, and Tokyo. The relative contribution of tree shade, air temperature reduction, and humidity increase on the AC energy reduction was further quantified. We found that well-watered trees provide the largest average summer AC energy reduction of −17% in the hot-dry climate (Riyadh, Phoenix). As tree shade is the dominant factor leading to the AC energy reduction in all city-climates, humid cities also show an average summer AC energy reduction ranging from −6% to −9%. However, increasing humidity is affecting AC dehumidification loads, especially under higher ventilation rates in humid climates and in these cities, AC energy reduction is most efficient with up to 40% tree cover. Additionally, we found that trees effectively reduce peak AC energy consumption due to higher shading effects in those hours. These results can inform urban planning strategies to maximize reduction in the AC energy demand using urban trees.","lang":"eng"}],"status":"public","DOAJ_listed":"1","citation":{"ama":"Meili N, Zheng X, Takane Y, et al. Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates. Journal of Advances in Modeling Earth Systems. 2025;17(3). doi:10.1029/2024ms004590","ista":"Meili N, Zheng X, Takane Y, Nakajima K, Yamaguchi K, Chi D, Zhu Y, Wang J, Qiu Y, Paschalis A, Manoli G, Burlando P, Tan PY, Fatichi S. 2025. Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates. Journal of Advances in Modeling Earth Systems. 17(3), e2024MS004590.","ieee":"N. Meili et al., “Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates,” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3. American Geophysical Union, 2025.","apa":"Meili, N., Zheng, X., Takane, Y., Nakajima, K., Yamaguchi, K., Chi, D., … Fatichi, S. (2025). Modeling the effect of trees on energy demand for indoor cooling and dehumidification across cities and climates. Journal of Advances in Modeling Earth Systems. American Geophysical Union. https://doi.org/10.1029/2024ms004590","short":"N. Meili, X. Zheng, Y. Takane, K. Nakajima, K. Yamaguchi, D. Chi, Y. Zhu, J. Wang, Y. Qiu, A. Paschalis, G. Manoli, P. Burlando, P.Y. Tan, S. Fatichi, Journal of Advances in Modeling Earth Systems 17 (2025).","mla":"Meili, Naika, et al. “Modeling the Effect of Trees on Energy Demand for Indoor Cooling and Dehumidification across Cities and Climates.” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3, e2024MS004590, American Geophysical Union, 2025, doi:10.1029/2024ms004590.","chicago":"Meili, Naika, Xing Zheng, Yuya Takane, Ko Nakajima, Kazuki Yamaguchi, Dengkai Chi, Yue Zhu, et al. “Modeling the Effect of Trees on Energy Demand for Indoor Cooling and Dehumidification across Cities and Climates.” Journal of Advances in Modeling Earth Systems. American Geophysical Union, 2025. https://doi.org/10.1029/2024ms004590."},"article_type":"original","language":[{"iso":"eng"}],"OA_place":"publisher","intvolume":" 17","date_updated":"2026-08-10T07:38:10Z","OA_type":"gold","author":[{"full_name":"Meili, Naika","first_name":"Naika","last_name":"Meili"},{"first_name":"Xing","last_name":"Zheng","full_name":"Zheng, Xing"},{"full_name":"Takane, Yuya","last_name":"Takane","first_name":"Yuya"},{"last_name":"Nakajima","first_name":"Ko","full_name":"Nakajima, Ko"},{"full_name":"Yamaguchi, Kazuki","last_name":"Yamaguchi","first_name":"Kazuki"},{"full_name":"Chi, Dengkai","last_name":"Chi","first_name":"Dengkai"},{"first_name":"Yue","last_name":"Zhu","full_name":"Zhu, Yue"},{"last_name":"Wang","first_name":"Jing","full_name":"Wang, Jing"},{"full_name":"Qiu, Yeshan","last_name":"Qiu","first_name":"Yeshan"},{"first_name":"Athanasios","last_name":"Paschalis","full_name":"Paschalis, Athanasios"},{"full_name":"Manoli, Gabriele","first_name":"Gabriele","last_name":"Manoli"},{"full_name":"Burlando, Paolo","last_name":"Burlando","first_name":"Paolo"},{"full_name":"Tan, Puay Yok","first_name":"Puay Yok","last_name":"Tan"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"}],"year":"2025","publication_status":"published","issue":"3","volume":17,"month":"03"},{"month":"09","related_material":{"record":[{"id":"18525","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","file_date_updated":"2026-08-07T10:57:34Z","year":"2025","page":"156","author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","first_name":"Natalia","last_name":"Ruzickova"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"E-Lib"}],"alternative_title":["ISTA Thesis"],"doi_confirm":"1","project":[{"_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e","name":"Collective behaviour of cells in pancreatic Islets of Langerhans"}],"ddc":["570","530"],"date_updated":"2026-08-10T07:47:56Z","OA_place":"publisher","language":[{"iso":"eng"}],"citation":{"ieee":"N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025.","ista":"Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria.","ama":"Ruzickova N. Effect propagation in biological networks. 2025. doi:10.15479/AT-ISTA-20357","apa":"Ruzickova, N. (2025). Effect propagation in biological networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20357","short":"N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025.","mla":"Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357.","chicago":"Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357."},"status":"public","has_accepted_license":"1","corr_author":"1","type":"dissertation","oa_version":"Published Version","date_created":"2025-09-15T17:04:48Z","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"day":"15","keyword":["gene regulation","networks","omnigenic model","pancreas","collective behaviour"],"title":"Effect propagation in biological networks","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-066-4"],"issn":["2663-337X"]},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-20357","acknowledgement":"I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n","file":[{"access_level":"closed","creator":"cchlebak","relation":"source_file","date_created":"2026-08-07T10:57:05Z","content_type":"application/x-zip-compressed","file_size":56464803,"file_id":"22661","file_name":"2025_Ruzickova_Natalia_Thesis.zip","date_updated":"2026-08-07T10:57:05Z","checksum":"0582508d439b233497384f83a8307398"},{"date_created":"2026-08-07T10:57:34Z","content_type":"application/pdf","access_level":"closed","relation":"main_file","creator":"cchlebak","embargo":"2026-09-15","date_updated":"2026-08-07T10:57:34Z","file_id":"22662","file_name":"2025_Ruzickova_Natalia_Thesis.pdf","checksum":"b722289fd550abede63adc27b9c61784","embargo_to":"open_access","file_size":30634378}],"_id":"20357","date_published":"2025-09-15T00:00:00Z","supervisor":[{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}]},{"publication_status":"published","file_date_updated":"2025-04-22T09:46:27Z","year":"2025","month":"04","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/pink-skies/"}],"record":[{"relation":"dissertation_contains","id":"20074","status":"public"}]},"issue":"1","volume":22,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","last_name":"Hübschmann","first_name":"Verena"},{"orcid":"0000-0003-4309-2251","first_name":"Medina","last_name":"Korkut","full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"full_name":"Maya-Arteaga, Juan Pablo","id":"c815d433-1f5d-11f0-a875-dad18b1e5924","first_name":"Juan Pablo","last_name":"Maya-Arteaga"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"pmid":1,"date_updated":"2026-08-12T08:45:16Z","ddc":["570"],"OA_place":"publisher","intvolume":" 22","project":[{"grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","name":"How human microglia shape developing neurons during health and inflammation"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"OA_type":"gold","abstract":[{"text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["40181459"],"isi":["001459311800002"]},"scopus_import":"1","publication":"Journal of Neuroinflammation","date_created":"2025-04-20T22:01:28Z","oa_version":"Published Version","corr_author":"1","type":"journal_article","citation":{"chicago":"Schmied, Verena, Medina Korkut, Alessandro Venturino, Juan Pablo Maya-Arteaga, and Sandra Siegert. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation. Springer Nature, 2025. https://doi.org/10.1186/s12974-025-03366-x.","short":"V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025).","mla":"Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation, vol. 22, no. 1, 98, Springer Nature, 2025, doi:10.1186/s12974-025-03366-x.","ista":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. 2025. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 22(1), 98.","ieee":"V. Schmied, M. Korkut, A. Venturino, J. P. Maya-Arteaga, and S. Siegert, “Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids,” Journal of Neuroinflammation, vol. 22, no. 1. Springer Nature, 2025.","ama":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 2025;22(1). doi:10.1186/s12974-025-03366-x","apa":"Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., & Siegert, S. (2025). Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. Springer Nature. https://doi.org/10.1186/s12974-025-03366-x"},"article_type":"original","DOAJ_listed":"1","language":[{"iso":"eng"}],"oa":1,"title":"Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"}],"day":"03","PlanS_conform":"1","publication_identifier":{"eissn":["1742-2094"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","APC_amount":"3948 EUR","publisher":"Springer Nature","file":[{"content_type":"application/pdf","date_created":"2025-04-22T09:46:27Z","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2025-04-22T09:46:27Z","file_id":"19607","file_name":"2025_JourNeuroinflammation_Schmied.pdf","success":1,"checksum":"dcc355c21ab713e45fda5c61b5fa5299","file_size":4482167}],"doi":"10.1186/s12974-025-03366-x","isi":1,"acknowledgement":"We thank the scientific service units at ISTA, specifically the Lab Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the Imaging and Optics Facility (IOF). We thank all members of the Siegert group and Marco Benevento for their constant feedback on the project and comments on the manuscript. A special thanks to Rouven Schulz for input on statistical analysis and sharing R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and Florianne Schoot Uiterkamp for their support in cell culture. This research was supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","article_number":"98","date_published":"2025-04-03T00:00:00Z","_id":"19593","quality_controlled":"1"},{"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development."}],"corr_author":"1","type":"dissertation","oa_version":"Published Version","date_created":"2025-07-24T12:37:22Z","language":[{"iso":"eng"}],"citation":{"apa":"Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074","ista":"Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria.","ama":"Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074","ieee":"V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025.","mla":"Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074.","short":"V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025.","chicago":"Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074."},"ddc":["570"],"date_updated":"2026-08-12T08:45:16Z","OA_place":"publisher","doi_confirm":"1","project":[{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"}],"author":[{"first_name":"Verena","last_name":"Hübschmann","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","full_name":"Hübschmann, Verena"}],"alternative_title":["ISTA Thesis"],"page":"151","file_date_updated":"2025-07-30T09:29:09Z","publication_status":"published","year":"2025","month":"07","related_material":{"record":[{"relation":"part_of_dissertation","id":"11478","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"19593"}]},"supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert"}],"_id":"20074","date_published":"2025-07-24T00:00:00Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-20074","file":[{"relation":"source_file","creator":"vhuebsch","access_level":"closed","date_created":"2025-07-30T08:47:53Z","content_type":"application/x-zip-compressed","file_size":43566093,"checksum":"d09f9984002353ad7442358394919bf3","date_updated":"2025-07-30T08:47:53Z","file_id":"20086","file_name":"PhD_Thesis_Schmied.zip"},{"date_created":"2025-07-30T08:47:46Z","content_type":"application/pdf","access_level":"open_access","creator":"vhuebsch","relation":"main_file","file_name":"PhD_Thesis_Schmied.pdf","file_id":"20087","date_updated":"2025-07-30T09:29:09Z","checksum":"4833690d7283c587f518ba98eeb2c946","file_size":13120922}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"isbn":["978-3-99078-060-2"],"issn":["2663-337X"]},"article_processing_charge":"No","title":"Human microglia impact neuronal development in retinal organoids","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"day":"24"},{"doi":"10.2140/pmp.2025.6.281","acknowledgement":"M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478.","publisher":"Mathematical Sciences Publishers","_id":"19372","date_published":"2025-02-23T00:00:00Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling","oa":1,"day":"23","department":[{"_id":"RoSe"}],"article_processing_charge":"No","publication_identifier":{"issn":["2690-0998"],"eissn":["2690-1005"]},"OA_place":"repository","intvolume":" 6","arxiv":1,"date_updated":"2026-08-12T08:44:53Z","OA_type":"green","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.16373"}],"type":"journal_article","oa_version":"Preprint","scopus_import":"1","date_created":"2025-03-09T23:01:28Z","publication":"Probability and Mathematical Physics","status":"public","external_id":{"arxiv":["2306.16373"]},"abstract":[{"text":"We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.","lang":"eng"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/pmp.2025.6.281.","apa":"Brooks, M., & Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2025.6.281","ieee":"M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” Probability and Mathematical Physics, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.","ama":"Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 2025;6(1):281-325. doi:10.2140/pmp.2025.6.281","ista":"Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325.","mla":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:10.2140/pmp.2025.6.281.","short":"M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325."},"year":"2025","publication_status":"published","volume":6,"issue":"1","month":"02","author":[{"orcid":"0000-0002-6249-0928","first_name":"Morris","last_name":"Brooks","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"}],"page":"281-325"},{"language":[{"iso":"eng"}],"DOAJ_listed":"1","citation":{"apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 2025;21(2). doi:10.46298/lmcs-21(2:2)2025","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” Logical Methods in Computer Science, vol. 21, no. 2. EPI Sciences, 2025.","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:10.46298/lmcs-21(2:2)2025.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025).","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025."},"article_type":"original","ec_funded":1,"status":"public","external_id":{"arxiv":["2307.06016"],"isi":["001468887900001"]},"has_accepted_license":"1","abstract":[{"text":"Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata.","lang":"eng"}],"corr_author":"1","type":"journal_article","oa_version":"Published Version","scopus_import":"1","publication":"Logical Methods in Computer Science","date_created":"2025-09-11T12:17:52Z","OA_type":"gold","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"arxiv":1,"ddc":["000"],"date_updated":"2026-08-12T08:46:05Z","OA_place":"publisher","intvolume":" 21","author":[{"first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","first_name":"Naci E"}],"month":"04","volume":21,"related_material":{"record":[{"id":"13221","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"20147"}]},"issue":"2","file_date_updated":"2025-09-11T12:17:12Z","publication_status":"published","year":"2025","article_number":"13149","quality_controlled":"1","_id":"20342","date_published":"2025-04-08T00:00:00Z","publisher":"EPI Sciences","doi":"10.46298/lmcs-21(2:2)2025","isi":1,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","file":[{"access_level":"open_access","creator":"esarac","relation":"main_file","content_type":"application/pdf","date_created":"2025-09-11T12:17:12Z","file_size":709584,"file_id":"20343","file_name":"2307.06016.pdf","date_updated":"2025-09-11T12:17:12Z","success":1,"checksum":"0b4d477bd981379724c35a4de2c176e5"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1860-5974"]},"PlanS_conform":"1","article_processing_charge":"Yes","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"day":"08","title":"Safety and liveness of quantitative properties and automata","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"A monitoring-oriented theory and classification of quantitative specifications","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"day":"07","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","doi":"10.15479/AT-ISTA-20147","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n","file":[{"file_size":8884801,"checksum":"0f3015f1db36576a23d8d669afb60b41","file_id":"20200","file_name":"2025_Sarac_NaciEge_Thesis.zip","date_updated":"2025-09-10T08:19:51Z","creator":"esarac","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","date_created":"2025-08-21T09:40:28Z"},{"file_size":2955584,"date_updated":"2025-08-21T09:40:34Z","file_name":"2025_Sarac_NaciEge_Thesis.pdf","file_id":"20201","success":1,"checksum":"332ed2fe61f580641664ec3f05d30f14","access_level":"open_access","relation":"main_file","creator":"esarac","content_type":"application/pdf","date_created":"2025-08-21T09:40:34Z"}],"supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"date_published":"2025-08-07T00:00:00Z","_id":"20147","publication_status":"published","file_date_updated":"2025-09-10T08:19:51Z","year":"2025","month":"08","publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","related_material":{"record":[{"id":"11775","status":"public","relation":"part_of_dissertation"},{"status":"deleted","id":"13140","relation":"part_of_dissertation"},{"status":"public","id":"19741","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"deleted","id":"19643"},{"id":"17634","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"13221","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9356","status":"public"},{"id":"20342","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac"}],"alternative_title":["ISTA Thesis"],"page":"149","ddc":["000"],"date_updated":"2026-08-12T08:46:04Z","OA_place":"publisher","doi_confirm":"1","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n\r\n","lang":"eng"}],"type":"dissertation","corr_author":"1","date_created":"2025-08-07T15:57:57Z","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"short":"N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025.","mla":"Sarac, Naci E. A Monitoring-Oriented Theory and Classification of Quantitative Specifications. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20147.","ama":"Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:10.15479/AT-ISTA-20147","ieee":"N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025.","ista":"Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria.","apa":"Sarac, N. E. (2025). A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20147","chicago":"Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20147."},"ec_funded":1},{"extern":"1","publisher":"Elsevier","doi":"10.1016/j.envsoft.2025.106603","das_tickbox":"1","article_number":"106603","_id":"22579","date_published":"2025-09-01T00:00:00Z","quality_controlled":"1","title":"VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","keyword":["VIC hydrologic model","Mekong river","Large-scale hydrology","Water resources management","Reservoir operations","Remote sensing"],"publication_identifier":{"eissn":["1873-6726"],"issn":["1364-8152"]},"article_processing_charge":"No","date_updated":"2026-08-12T09:07:29Z","intvolume":" 193","OA_type":"closed access","abstract":[{"text":"Decades of research on the Mekong River basin have vastly expanded our knowledge of key hydrological and\r\necological processes, in part thanks to the development of modelling tools. However, few of these models are\r\nopenly available to the research community or adhere to FAIR (Findable, Accessible, Interoperable, Reusable)\r\nprinciples, particularly in the domain of hydrology, in turn limiting transparency, reproducibility, and broader\r\nscientific engagement. Here, we address this gap and introduce VIC-Res Mekong, an open-source hydrologicalwater management model for the Mekong River basin. The model is implemented over a spatial domain\r\nof ∼630,000 km2 and has a resolution of 0.0625 degrees. Water and energy budgets are simulated with\r\nthe Variable Infiltration Capacity (VIC) model, while streamflow routing is simulated with VIC-Res, which\r\nexplicitly accounts for the storage and release dynamics of reservoirs. This is of key importance for a basin\r\nlike the Mekong, where the active storage capacity of dams has increased from 20 km3 to nearly 80 km3 in the past fifteen years. To this purpose, VIC-Res Mekong integrates information from a database containing reservoir storage time series (inferred from satellite images) for 129 dams that accounts for more than 90% of total storage capacity. These data support both hindcast simulations and the derivation of reservoir operating rules, enabling a flexible and realistic representation of dam operations that allows to characterize in detail dam-induced hydrological alterations.","lang":"eng"}],"status":"public","oa_version":"None","scopus_import":"1","publication":"Environmental Modelling & Software","date_created":"2026-07-27T12:30:25Z","type":"journal_article","citation":{"chicago":"Eldardiry, Hisham, Shanti Shwarup Mahto, Simone Fatichi, and Stefano Galelli. “VIC-Res Mekong: An Open-Source Hydrological-Water Management Model for the Mekong River Basin.” Environmental Modelling & Software. Elsevier, 2025. https://doi.org/10.1016/j.envsoft.2025.106603.","ama":"Eldardiry H, Mahto SS, Fatichi S, Galelli S. VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin. Environmental Modelling & Software. 2025;193. doi:10.1016/j.envsoft.2025.106603","ieee":"H. Eldardiry, S. S. Mahto, S. Fatichi, and S. Galelli, “VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin,” Environmental Modelling & Software, vol. 193. Elsevier, 2025.","ista":"Eldardiry H, Mahto SS, Fatichi S, Galelli S. 2025. VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin. Environmental Modelling & Software. 193, 106603.","apa":"Eldardiry, H., Mahto, S. S., Fatichi, S., & Galelli, S. (2025). VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin. Environmental Modelling & Software. Elsevier. https://doi.org/10.1016/j.envsoft.2025.106603","short":"H. Eldardiry, S.S. Mahto, S. Fatichi, S. Galelli, Environmental Modelling & Software 193 (2025).","mla":"Eldardiry, Hisham, et al. “VIC-Res Mekong: An Open-Source Hydrological-Water Management Model for the Mekong River Basin.” Environmental Modelling & Software, vol. 193, 106603, Elsevier, 2025, doi:10.1016/j.envsoft.2025.106603."},"article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","year":"2025","month":"09","volume":193,"author":[{"last_name":"Eldardiry","first_name":"Hisham","full_name":"Eldardiry, Hisham"},{"full_name":"Mahto, Shanti Shwarup","first_name":"Shanti Shwarup","last_name":"Mahto"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"},{"full_name":"Galelli, Stefano","first_name":"Stefano","last_name":"Galelli"}]},{"date_created":"2026-07-27T12:30:25Z","publication":"npj Natural Hazards","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/s44304-025-00148-6","open_access":"1"}],"type":"journal_article","abstract":[{"text":"Extreme rainfall events that break previous records are occurring more frequently worldwide, leading to severe flooding and infrastructure damage. Conventional flood design approaches, based on extreme value analysis (EVA) of limited historical data, often fail to anticipate such unprecedented extremes. Here, we present a stochastic approach that leverages the Advanced Weather Generator (AWE-GEN) to simulate a large ensemble of 100-year hourly rainfall time series, explicitly accounting for internal climate variability. By excluding the record-breaking event year during calibration, we assess the ability of our proposed method to reproduce unseen record-breaking events. We evaluated this approach using data from 2703 rain stations across nine countries. Our results show that the stochastic approach captures record-breaking events more reliably than EVA, achieving success rates exceeding 85% for 3–12-hour durations at a 100-year return period threshold. This framework provides a more robust way for estimating rainfall extremes and supports the design of resilient infrastructure under deep uncertainty.","lang":"eng"}],"status":"public","citation":{"apa":"Chen, M., Mahto, S. S., He, X., Jun, C., Paschalis, A., Peleg, N., … Fatichi, S. (2025). Record-breaking rainfall: a stochastic approach for its prediction. Npj Natural Hazards. Springer Nature. https://doi.org/10.1038/s44304-025-00148-6","ista":"Chen M, Mahto SS, He X, Jun C, Paschalis A, Peleg N, Mascaro G, Fatichi S. 2025. Record-breaking rainfall: a stochastic approach for its prediction. npj Natural Hazards. 2, 98.","ama":"Chen M, Mahto SS, He X, et al. Record-breaking rainfall: a stochastic approach for its prediction. npj Natural Hazards. 2025;2. doi:10.1038/s44304-025-00148-6","ieee":"M. Chen et al., “Record-breaking rainfall: a stochastic approach for its prediction,” npj Natural Hazards, vol. 2. Springer Nature, 2025.","mla":"Chen, Mengzhu, et al. “Record-Breaking Rainfall: A Stochastic Approach for Its Prediction.” Npj Natural Hazards, vol. 2, 98, Springer Nature, 2025, doi:10.1038/s44304-025-00148-6.","short":"M. Chen, S.S. Mahto, X. He, C. Jun, A. Paschalis, N. Peleg, G. Mascaro, S. Fatichi, Npj Natural Hazards 2 (2025).","chicago":"Chen, Mengzhu, Shanti Shwarup Mahto, Xiaogang He, Changhyun Jun, Athanasios Paschalis, Nadav Peleg, Giuseppe Mascaro, and Simone Fatichi. “Record-Breaking Rainfall: A Stochastic Approach for Its Prediction.” Npj Natural Hazards. Springer Nature, 2025. https://doi.org/10.1038/s44304-025-00148-6."},"DOAJ_listed":"1","article_type":"original","language":[{"iso":"eng"}],"OA_place":"publisher","intvolume":" 2","date_updated":"2026-08-12T08:59:35Z","OA_type":"gold","author":[{"first_name":"Mengzhu","last_name":"Chen","full_name":"Chen, Mengzhu"},{"first_name":"Shanti Shwarup","last_name":"Mahto","full_name":"Mahto, Shanti Shwarup"},{"last_name":"He","first_name":"Xiaogang","full_name":"He, Xiaogang"},{"full_name":"Jun, Changhyun","last_name":"Jun","first_name":"Changhyun"},{"full_name":"Paschalis, Athanasios","last_name":"Paschalis","first_name":"Athanasios"},{"full_name":"Peleg, Nadav","last_name":"Peleg","first_name":"Nadav"},{"last_name":"Mascaro","first_name":"Giuseppe","full_name":"Mascaro, Giuseppe"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone"}],"year":"2025","publication_status":"published","volume":2,"month":"10","das_tickbox":"1","date_published":"2025-10-29T00:00:00Z","_id":"22586","quality_controlled":"1","article_number":"98","extern":"1","doi":"10.1038/s44304-025-00148-6","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"eissn":["2948-2100"]},"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"Record-breaking rainfall: a stochastic approach for its prediction","day":"29"},{"date_published":"2025-05-01T00:00:00Z","_id":"19701","quality_controlled":"1","publisher":"Annual Reviews","doi":"10.1146/annurev-biophys-060524-102720","file":[{"file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","file_id":"19710","date_updated":"2025-05-19T07:55:51Z","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","success":1,"file_size":317925,"content_type":"application/pdf","date_created":"2025-05-19T07:55:51Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","isi":1,"publication_identifier":{"eissn":["1936-1238"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"GaTk"}],"day":"01","oa":1,"title":"Information processing in biochemical networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:10.1146/annurev-biophys-060524-102720.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. Annual Review of Biophysics. 2025;54:249-274. doi:10.1146/annurev-biophys-060524-102720","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274.","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” Annual Review of Biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025.","apa":"Tkačik, G., & Wolde, P. R. T. (2025). Information processing in biochemical networks. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-060524-102720","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-biophys-060524-102720."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components."}],"status":"public","external_id":{"isi":["001488641500013"],"pmid":["39929539"]},"has_accepted_license":"1","date_created":"2025-05-18T22:02:50Z","oa_version":"Published Version","publication":"Annual Review of Biophysics","scopus_import":"1","type":"journal_article","corr_author":"1","OA_type":"hybrid","project":[{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"date_updated":"2026-08-12T09:25:42Z","ddc":["570"],"intvolume":" 54","OA_place":"publisher","page":"249-274","pmid":1,"author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Wolde","first_name":"Pieter Rein Ten","full_name":"Wolde, Pieter Rein Ten"}],"month":"05","volume":54,"publication_status":"published","file_date_updated":"2025-05-19T07:55:51Z","year":"2025"},{"date_published":"2025-06-27T00:00:00Z","_id":"20048","quality_controlled":"1","article_number":"dev204261","acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","isi":1,"file":[{"file_id":"20070","file_name":"2025_Development_Moriyama.pdf","date_updated":"2025-07-23T08:43:01Z","checksum":"808d8aa28df79d23fb661838d1fdc1be","success":1,"file_size":25935563,"content_type":"application/pdf","date_created":"2025-07-23T08:43:01Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"doi":"10.1242/dev.204261","publisher":"Company of Biologists","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"PlanS_conform":"1","day":"27","department":[{"_id":"CaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","oa":1,"language":[{"iso":"eng"}],"citation":{"short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:10.1242/dev.204261.","ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” Development, vol. 152, no. 12. Company of Biologists, 2025.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 2025;152(12). doi:10.1242/dev.204261","apa":"Moriyama, Y., Mitsui, T., & Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.204261","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development. Company of Biologists, 2025. https://doi.org/10.1242/dev.204261."},"article_type":"original","type":"journal_article","corr_author":"1","oa_version":"Published Version","date_created":"2025-07-21T08:10:32Z","scopus_import":"1","publication":"Development","external_id":{"isi":["001525252300001"],"pmid":["40576478"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations."}],"OA_type":"hybrid","intvolume":" 152","OA_place":"publisher","ddc":["570"],"date_updated":"2026-08-12T10:01:31Z","pmid":1,"author":[{"orcid":"0000-0002-2853-8051","first_name":"Yuuta","last_name":"Moriyama","full_name":"Moriyama, Yuuta","id":"addc9b8c-67a0-11f0-b374-a2e094825470"},{"full_name":"Mitsui, Toshiyuki","first_name":"Toshiyuki","last_name":"Mitsui"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"volume":152,"issue":"12","month":"06","year":"2025","publication_status":"published","file_date_updated":"2025-07-23T08:43:01Z"},{"volume":12,"month":"10","year":"2025","publication_status":"published","file_date_updated":"2026-02-24T07:56:34Z","page":"1677-1691","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"},{"orcid":"0000-0001-8467-4106","first_name":"Yik Tung","last_name":"Chan","full_name":"Chan, Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1"}],"OA_type":"gold","project":[{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"OA_place":"publisher","intvolume":" 12","ddc":["510"],"arxiv":1,"date_updated":"2026-08-12T11:17:50Z","supplementarymaterial":"no","language":[{"iso":"eng"}],"citation":{"chicago":"Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2025. https://doi.org/10.5802/jep.320.","mla":"Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:10.5802/jep.320.","short":"T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691.","apa":"Browning, T. D., & Chan, S. (2025). Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.320","ista":"Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.","ieee":"T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025.","ama":"Browning TD, Chan S. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 2025;12:1677-1691. doi:10.5802/jep.320"},"article_type":"original","DOAJ_listed":"1","type":"journal_article","corr_author":"1","oa_version":"Published Version","publication":"Journal de l'Ecole Polytechnique - Mathematiques","scopus_import":"1","date_created":"2026-02-22T23:01:36Z","status":"public","has_accepted_license":"1","external_id":{"arxiv":["2411.09264"]},"abstract":[{"lang":"eng","text":"The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given"},{"lang":"fre","text":" Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques."}],"researchdata_availability":"no","day":"21","department":[{"_id":"TiBr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Solubility of a resultant equation and applications","oa":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"doi":"10.5802/jep.320","acknowledgement":"While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278).","file":[{"date_updated":"2026-02-24T07:56:34Z","file_name":"2025_JEP_Browning.pdf","file_id":"21356","checksum":"828577ea48ac6109d3e9dd1aeddd45c4","success":1,"file_size":1003689,"content_type":"application/pdf","date_created":"2026-02-24T07:56:34Z","access_level":"open_access","relation":"main_file","creator":"dernst"}],"publisher":"Ecole Polytechnique","date_published":"2025-10-21T00:00:00Z","_id":"21343","quality_controlled":"1","das_tickbox":"0"},{"author":[{"last_name":"Browning","orcid":"0000-0002-8314-0177","first_name":"Timothy D","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch","first_name":"Florian Alexander","orcid":"0000-0001-7302-8256"}],"dataavailabilitystatement":"The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page.","file_date_updated":"2025-09-03T06:44:44Z","publication_status":"published","year":"2025","month":"09","issue":"4","related_material":{"record":[{"id":"22234","status":"public","relation":"research_data"}],"link":[{"url":"https://github.com/fwilsch/cubicpts","relation":"software"}]},"volume":31,"abstract":[{"lang":"eng","text":"We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces."}],"status":"public","external_id":{"arxiv":["2407.16315"],"isi":["001552779800001"]},"has_accepted_license":"1","publication":"Selecta Mathematica New Series","oa_version":"Published Version","date_created":"2025-08-31T22:01:31Z","scopus_import":"1","corr_author":"1","type":"journal_article","citation":{"chicago":"Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series. Springer Nature, 2025. https://doi.org/10.1007/s00029-025-01074-1.","short":"T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).","mla":"Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series, vol. 31, no. 4, 81, Springer Nature, 2025, doi:10.1007/s00029-025-01074-1.","ista":"Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.","ieee":"T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” Selecta Mathematica New Series, vol. 31, no. 4. Springer Nature, 2025.","ama":"Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 2025;31(4). doi:10.1007/s00029-025-01074-1","apa":"Browning, T. D., & Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. Springer Nature. https://doi.org/10.1007/s00029-025-01074-1"},"article_type":"original","language":[{"iso":"eng"}],"supplementarymaterial":"yes","date_updated":"2026-08-12T12:15:32Z","ddc":["500"],"arxiv":1,"OA_place":"publisher","intvolume":" 31","project":[{"name":"New frontiers of the Manin conjecture","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P32428"},{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"OA_type":"hybrid","PlanS_conform":"1","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","oa":1,"title":"Integral points on cubic surfaces: heuristics and numerics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiBr"}],"researchdata_availability":"yes","day":"01","das_tickbox":"1","article_number":"81","date_published":"2025-09-01T00:00:00Z","_id":"20249","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","file":[{"checksum":"89352f1f7e8d2b367ae5f4e9bf9eb1f5","success":1,"file_name":"2025_SelectaMathematica_Browning.pdf","file_id":"20281","date_updated":"2025-09-03T06:44:44Z","file_size":2484757,"content_type":"application/pdf","date_created":"2025-09-03T06:44:44Z","creator":"dernst","relation":"main_file","access_level":"open_access"}],"doi":"10.1007/s00029-025-01074-1","isi":1}]