---
OA_type: closed access
_id: '20704'
abstract:
- lang: eng
text: Generative models have advanced significantly in sampling material systems
with continuous variables, such as atomistic structures. However, their application
to discrete variables, like atom types or spin states, remains underexplored.
In this work, we introduce a discrete flow matching model, tailored for systems
with discrete phase-space coordinates (e.g., the Ising model or a multicomponent
system on a lattice). This approach enables a single model to sample free energy
surfaces over a wide temperature range with minimal training overhead, and the
model generation is scalable to larger lattice sizes than those in the training
set. We demonstrate our approach on the 2D Ising model, showing efficient and
reliable free energy sampling. These results highlight the potential of flow matching
for low-cost, scalable free energy sampling in discrete systems and suggest promising
extensions to alchemical degrees of freedom in crystalline materials. The codebase
developed for this work is openly available at https://github.com/tuoping/alchemicalFES.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral
Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413.
The authors acknowledge the research computing facilities provided by the Institute
of Science and Technology Austria (ISTA), and resources of the National Energy Research
Scientific Computing Center (NERSC), a Department of Energy Office of Science User
Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued
discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.
article_processing_charge: No
article_type: original
author:
- first_name: Ping
full_name: Tuo, Ping
id: 6e5644c0-c180-11ed-a2da-facc4c9f4f09
last_name: Tuo
- first_name: Zezhu
full_name: Zeng, Zezhu
id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
last_name: Zeng
orcid: 0000-0001-5126-4928
- first_name: Jiale
full_name: Chen, Jiale
id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785
last_name: Chen
orcid: 0000-0001-5337-5875
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling
of classical Ising spin states. Journal of Chemical Theory and Computation.
2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248
apa: Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature
free energy sampling of classical Ising spin states. Journal of Chemical Theory
and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248
chicago: Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature
Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory
and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248.
ieee: P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy
sampling of classical Ising spin states,” Journal of Chemical Theory and Computation,
vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.
ista: Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy
sampling of classical Ising spin states. Journal of Chemical Theory and Computation.
21(22), 11427–11435.
mla: Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical
Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21,
no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248.
short: P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation
21 (2025) 11427–11435.
corr_author: '1'
das_tickbox: '0'
date_created: 2025-11-30T23:02:06Z
date_published: 2025-10-31T00:00:00Z
date_updated: 2026-08-07T10:29:06Z
day: '31'
department:
- _id: BiCh
- _id: DaAl
doi: 10.1021/acs.jctc.5c01248
ec_funded: 1
external_id:
isi:
- '001605927900001'
pmid:
- '41172130'
intvolume: ' 21'
isi: 1
issue: '22'
language:
- iso: eng
month: '10'
oa_version: None
page: 11427-11435
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/tuoping/alchemicalFES
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Scalable multitemperature free energy sampling of classical Ising spin states
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22525'
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."
article_processing_charge: No
article_type: original
author:
- first_name: Jordi
full_name: Buckley Paules, Jordi
last_name: Buckley Paules
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Bonnie
full_name: Warring, Bonnie
last_name: Warring
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
citation:
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'
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'
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.'
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.'
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.'
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.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-03-03T00:00:00Z
date_updated: 2026-08-07T10:31:51Z
day: '03'
doi: 10.5194/gmd-18-1287-2025
extern: '1'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.5194/gmd-18-1287-2025
month: '03'
oa: 1
oa_version: Published Version
page: 1287-1305
publication: Geoscientific Model Development
publication_identifier:
eissn:
- 1991-9603
issn:
- 1991-959X
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'T&C-CROP: representing mechanistic crop growth with a terrestrial biosphere
model (T&C, v1.5) – model formulation and validation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 18
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22557'
abstract:
- lang: eng
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."
article_processing_charge: No
article_type: original
author:
- first_name: Yiran
full_name: Wang, Yiran
last_name: Wang
- first_name: Naika
full_name: Meili, Naika
last_name: Meili
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
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
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
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.
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.
ista: Wang Y, Meili N, Fatichi S. 2025. Ecohydrological responses to solar radiation
changes. Hydrology and Earth System Sciences. 29(2), 381–396.
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.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-01-21T00:00:00Z
date_updated: 2026-08-07T10:42:02Z
day: '21'
doi: 10.5194/hess-29-381-2025
extern: '1'
intvolume: ' 29'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.5194/hess-29-381-2025
month: '01'
oa: 1
oa_version: Published Version
page: 381-396
publication: Hydrology and Earth System Sciences
publication_identifier:
eissn:
- 1607-7938
issn:
- 1027-5606
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ecohydrological responses to solar radiation changes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 29
year: '2025'
...
---
OA_type: closed access
_id: '22539'
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."
article_number: '134000'
article_processing_charge: No
article_type: original
author:
- first_name: Yexia
full_name: Lin Xu, Yexia
last_name: Lin Xu
- first_name: Naika
full_name: Meili, Naika
last_name: Meili
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
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'
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'
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.'
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.'
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.'
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).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-08-07T10:37:29Z
day: '01'
doi: 10.1016/j.jhydrol.2025.134000
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
publication: Journal of Hydrology
publication_identifier:
eissn:
- 1879-2707
issn:
- 0022-1694
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Long-term hydrological budget over urban areas: approaches and challenges'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 662, Part B
year: '2025'
...
---
OA_type: closed access
_id: '22562'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Liangzhi
full_name: Chen, Liangzhi
last_name: Chen
- first_name: Philipp
full_name: Brun, Philipp
last_name: Brun
- first_name: Pascal
full_name: Buri, Pascal
last_name: Buri
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Arthur
full_name: Gessler, Arthur
last_name: Gessler
- first_name: Michael James
full_name: McCarthy, Michael James
last_name: McCarthy
- first_name: Francesca
full_name: Pellicciotti, Francesca
last_name: Pellicciotti
- first_name: Benjamin
full_name: Stocker, Benjamin
last_name: Stocker
- first_name: Dirk Nikolaus
full_name: Karger, Dirk Nikolaus
last_name: Karger
citation:
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
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
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.
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.
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.
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.
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.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-01-17T00:00:00Z
date_updated: 2026-08-07T10:47:08Z
day: '17'
doi: 10.1126/science.ado4245
extern: '1'
intvolume: ' 387'
issue: '6731'
language:
- iso: eng
month: '01'
oa_version: None
page: 278-284
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global increase in the occurrence and impact of multiyear droughts
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 387
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22568'
abstract:
- lang: eng
text: "The recent surge in reservoir construction has increased global surface water
storage, with Mainland\r\nSoutheast Asia (MSEA) being a significant hotspot. Such
infrastructural evolution demands updates in water\r\nmanagement strategies and
hydrological models. However, information on actual reservoir storage is hard
to\r\nacquire, especially for transboundary river basins. To date, no high-resolution
spatiotemporal dataset on absolute\r\nstorage time series is available for reservoirs
in MSEA. To address this gap, we present (1) a comprehensive openaccess database
of absolute storage time series (sub-monthly) for 186 reservoirs (larger than
0.1 km3) in MSEA\r\nspanning the period 1985–2023 and (2) an analysis of the reservoir
storage dynamics. This dataset is derived\r\nfrom remote sensing observations,
integrating satellite-based water surface area extraction from high-resolution\r\n(30
m) images and area–elevation–storage (A–E–S) relationships to estimate reservoir
level and storage dynamics. The MSEA database includes static (area–elevation–storage
curves, water frequency, and reservoir extent)\r\nand dynamic (area, water level,
and absolute storage time series) components for each reservoir. The 186 reservoirs
collectively store around 175 km3 of water, with a minimum of 140 km3 and a maximum
of 210 km3. They\r\ncover an average area of 8700 km2, ranging from a minimum
of 6500 km2 to a maximum of 10 000 km2. We show that the combined average reservoir
storage increased from 70 to 160 km3 (+130 %) from 2008 to 2017, primarily contributed
by reservoirs in the Irrawaddy, Red, Upper Mekong, and Lower Mekong basins. Our
in situ validation provides a good match between estimated storage and in situ
observations, with 50 % of the validation sites (10 out of 20) showing an R2 >
0.7 and an average nRMSE < 14 %. The indirect validation (based on altimetry-converted
storage) shows even better results, with an R2 > 0.7 and an average nRMSE < 12
% for 70 % (14 out of 20) of the reservoirs. Furthermore, the analysis of the
2019–2020 drought event in the MSEA region reveals that nearly 30 %–40 % of the
region experienced more than 5 months of drought, with the most significant impact
on reservoirs in Cambodia and Thailand. As a result, storage departures ranged
by up to −40 % in some reservoirs, highlighting significant impacts on water availability.
Overall, this analysis demonstrates the potential of the inferred storage time
series for assessing real-life water-related problems in Mainland Southeast Asia,
with the possibility of applying the method to estimate reservoir storage time
series in other parts of the world. The reservoir storage database in Mainland
Southeast Asia (MSEA-Res database) and the associated Python code are publicly
available on Zenodo at https://doi.org/10.5281/zenodo.14844580 (Mahto et al.,
2025)."
article_processing_charge: No
article_type: original
author:
- first_name: Shanti Shwarup
full_name: Mahto, Shanti Shwarup
last_name: Mahto
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Stefano
full_name: Galelli, Stefano
last_name: Galelli
citation:
ama: Mahto SS, Fatichi S, Galelli S. A 1985–2023 time series dataset of absolute
reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science
Data. 2025;17(6):2693-2712. doi:10.5194/essd-17-2693-2025
apa: Mahto, S. S., Fatichi, S., & Galelli, S. (2025). A 1985–2023 time series
dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth
System Science Data. Copernicus Publications. https://doi.org/10.5194/essd-17-2693-2025
chicago: Mahto, Shanti Shwarup, Simone Fatichi, and Stefano Galelli. “A 1985–2023
Time Series Dataset of Absolute Reservoir Storage in Mainland Southeast Asia (MSEA-Res).”
Earth System Science Data. Copernicus Publications, 2025. https://doi.org/10.5194/essd-17-2693-2025.
ieee: S. S. Mahto, S. Fatichi, and S. Galelli, “A 1985–2023 time series dataset
of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res),” Earth
System Science Data, vol. 17, no. 6. Copernicus Publications, pp. 2693–2712,
2025.
ista: Mahto SS, Fatichi S, Galelli S. 2025. A 1985–2023 time series dataset of absolute
reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science
Data. 17(6), 2693–2712.
mla: Mahto, Shanti Shwarup, et al. “A 1985–2023 Time Series Dataset of Absolute
Reservoir Storage in Mainland Southeast Asia (MSEA-Res).” Earth System Science
Data, vol. 17, no. 6, Copernicus Publications, 2025, pp. 2693–712, doi:10.5194/essd-17-2693-2025.
short: S.S. Mahto, S. Fatichi, S. Galelli, Earth System Science Data 17 (2025) 2693–2712.
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-06-17T00:00:00Z
date_updated: 2026-08-07T10:54:05Z
day: '17'
doi: 10.5194/essd-17-2693-2025
extern: '1'
intvolume: ' 17'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.5194/essd-17-2693-2025
month: '06'
oa: 1
oa_version: Published Version
page: 2693-2712
publication: Earth System Science Data
publication_identifier:
eissn:
- 1866-3516
issn:
- 1866-3508
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast
Asia (MSEA-Res)
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 17
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '22572'
abstract:
- lang: eng
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.'
article_number: '107018'
article_processing_charge: No
article_type: original
author:
- first_name: Yue
full_name: Zhu, Yue
last_name: Zhu
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Ye
full_name: Zhang, Ye
last_name: Zhang
- first_name: Dengkai
full_name: Chi, Dengkai
last_name: Chi
- first_name: Jing
full_name: Wang, Jing
last_name: Wang
- first_name: Yeshan
full_name: Qiu, Yeshan
last_name: Qiu
- first_name: Matteo
full_name: Bonatesta, Matteo
last_name: Bonatesta
- first_name: Wenyue
full_name: Zou, Wenyue
last_name: Zou
- first_name: Christian
full_name: Geiß, Christian
last_name: Geiß
- first_name: Puay Yok
full_name: Tan, Puay Yok
last_name: Tan
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
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
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
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.
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.
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.
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.
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).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-12-15T00:00:00Z
date_updated: 2026-08-07T10:58:46Z
day: '15'
doi: 10.1016/j.scs.2025.107018
extern: '1'
intvolume: ' 135'
keyword:
- Urban morphology
- Urban expansion
- Pluvial flood
- Flood resilience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.scs.2025.107018
month: '12'
oa: 1
oa_version: Published Version
publication: Sustainable Cities and Society
publication_identifier:
eissn:
- 2210-6715
issn:
- 2210-6707
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of urban morphological changes on pluvial flooding during urban
expansion
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 135
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22499'
abstract:
- lang: eng
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.
article_number: e2024MS004590
article_processing_charge: No
article_type: original
author:
- first_name: Naika
full_name: Meili, Naika
last_name: Meili
- first_name: Xing
full_name: Zheng, Xing
last_name: Zheng
- first_name: Yuya
full_name: Takane, Yuya
last_name: Takane
- first_name: Ko
full_name: Nakajima, Ko
last_name: Nakajima
- first_name: Kazuki
full_name: Yamaguchi, Kazuki
last_name: Yamaguchi
- first_name: Dengkai
full_name: Chi, Dengkai
last_name: Chi
- first_name: Yue
full_name: Zhu, Yue
last_name: Zhu
- first_name: Jing
full_name: Wang, Jing
last_name: Wang
- first_name: Yeshan
full_name: Qiu, Yeshan
last_name: Qiu
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
- first_name: Gabriele
full_name: Manoli, Gabriele
last_name: Manoli
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Puay Yok
full_name: Tan, Puay Yok
last_name: Tan
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
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
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
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.
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.
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.
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.
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).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2026-08-10T07:38:10Z
day: '01'
doi: 10.1029/2024ms004590
extern: '1'
intvolume: ' 17'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2024MS004590
month: '03'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling the effect of trees on energy demand for indoor cooling and dehumidification
across cities and climates
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 17
year: '2025'
...
---
OA_place: publisher
_id: '20357'
acknowledged_ssus:
- _id: ScienComp
- _id: E-Lib
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"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
citation:
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
chicago: Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357.
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.
mla: Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357.
short: N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-09-15T17:04:48Z
date_published: 2025-09-15T00:00:00Z
date_updated: 2026-08-10T07:47:56Z
day: '15'
ddc:
- '570'
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaTk
doi: 10.15479/AT-ISTA-20357
doi_confirm: '1'
file:
- access_level: closed
checksum: 0582508d439b233497384f83a8307398
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2026-08-07T10:57:05Z
date_updated: 2026-08-07T10:57:05Z
file_id: '22661'
file_name: 2025_Ruzickova_Natalia_Thesis.zip
file_size: 56464803
relation: source_file
- access_level: closed
checksum: b722289fd550abede63adc27b9c61784
content_type: application/pdf
creator: cchlebak
date_created: 2026-08-07T10:57:34Z
date_updated: 2026-08-07T10:57:34Z
embargo: 2026-09-15
embargo_to: open_access
file_id: '22662'
file_name: 2025_Ruzickova_Natalia_Thesis.pdf
file_size: 30634378
relation: main_file
file_date_updated: 2026-08-07T10:57:34Z
has_accepted_license: '1'
keyword:
- gene regulation
- networks
- omnigenic model
- pancreas
- collective behaviour
language:
- iso: eng
month: '09'
oa_version: Published Version
page: '156'
project:
- _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e
name: Collective behaviour of cells in pancreatic Islets of Langerhans
publication_identifier:
isbn:
- 978-3-99078-066-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '18525'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Effect propagation in biological networks
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
APC_amount: 3948 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '19593'
abstract:
- lang: eng
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.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
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'
article_processing_charge: Yes
article_type: original
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
- first_name: Medina
full_name: Korkut, Medina
id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
last_name: Korkut
orcid: 0000-0003-4309-2251
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Juan Pablo
full_name: Maya-Arteaga, Juan Pablo
id: c815d433-1f5d-11f0-a875-dad18b1e5924
last_name: Maya-Arteaga
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
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
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.
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.
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.
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.
short: V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal
of Neuroinflammation 22 (2025).
corr_author: '1'
date_created: 2025-04-20T22:01:28Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2026-08-12T08:45:16Z
day: '03'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1186/s12974-025-03366-x
external_id:
isi:
- '001459311800002'
pmid:
- '40181459'
file:
- access_level: open_access
checksum: dcc355c21ab713e45fda5c61b5fa5299
content_type: application/pdf
creator: dernst
date_created: 2025-04-22T09:46:27Z
date_updated: 2025-04-22T09:46:27Z
file_id: '19607'
file_name: 2025_JourNeuroinflammation_Schmied.pdf
file_size: 4482167
relation: main_file
success: 1
file_date_updated: 2025-04-22T09:46:27Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Journal of Neuroinflammation
publication_identifier:
eissn:
- 1742-2094
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/pink-skies/
record:
- id: '20074'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Microglia determine an immune-challenged environment and facilitate ibuprofen
action in human retinal organoids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2025'
...
---
OA_place: publisher
_id: '20074'
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."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Verena
full_name: Hübschmann, Verena
id: 32B7C918-F248-11E8-B48F-1D18A9856A87
last_name: Hübschmann
citation:
ama: Schmied V. Human microglia impact neuronal development in retinal organoids.
2025. doi:10.15479/AT-ISTA-20074
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
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.
ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,”
Institute of Science and Technology Austria, 2025.
ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids.
Institute of Science and Technology Austria.
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.
corr_author: '1'
date_created: 2025-07-24T12:37:22Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2026-08-12T08:45:16Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: SaSi
doi: 10.15479/AT-ISTA-20074
doi_confirm: '1'
file:
- access_level: closed
checksum: d09f9984002353ad7442358394919bf3
content_type: application/x-zip-compressed
creator: vhuebsch
date_created: 2025-07-30T08:47:53Z
date_updated: 2025-07-30T08:47:53Z
file_id: '20086'
file_name: PhD_Thesis_Schmied.zip
file_size: 43566093
relation: source_file
- access_level: open_access
checksum: 4833690d7283c587f518ba98eeb2c946
content_type: application/pdf
creator: vhuebsch
date_created: 2025-07-30T08:47:46Z
date_updated: 2025-07-30T09:29:09Z
file_id: '20087'
file_name: PhD_Thesis_Schmied.pdf
file_size: 13120922
relation: main_file
file_date_updated: 2025-07-30T09:29:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
grant_number: SC19-017
name: How human microglia shape developing neurons during health and inflammation
publication_identifier:
isbn:
- 978-3-99078-060-2
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11478'
relation: part_of_dissertation
status: public
- id: '19593'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
title: Human microglia impact neuronal development in retinal organoids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19372'
abstract:
- lang: eng
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.
acknowledgement: M.B. gratefully acknowledges funding from the ERC Advanced Grant
ERC-AdG CLaQS, grant agreement n. 83478.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Morris
full_name: Brooks, Morris
id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425
last_name: Brooks
orcid: 0000-0002-6249-0928
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
citation:
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
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
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.
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.
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.
corr_author: '1'
date_created: 2025-03-09T23:01:28Z
date_published: 2025-02-23T00:00:00Z
date_updated: 2026-08-12T08:44:53Z
day: '23'
department:
- _id: RoSe
doi: 10.2140/pmp.2025.6.281
external_id:
arxiv:
- '2306.16373'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2306.16373
month: '02'
oa: 1
oa_version: Preprint
page: 281-325
publication: Probability and Mathematical Physics
publication_identifier:
eissn:
- 2690-1005
issn:
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymptotic series for low-energy excitations of the Fröhlich polaron at strong
coupling
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20342'
abstract:
- lang: eng
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.
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.
article_number: '13149'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Nicolas Adrien
full_name: Mazzocchi, Nicolas Adrien
id: b26baa86-3308-11ec-87b0-8990f34baa85
last_name: Mazzocchi
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
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
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
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.
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.
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.
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).
corr_author: '1'
date_created: 2025-09-11T12:17:52Z
date_published: 2025-04-08T00:00:00Z
date_updated: 2026-08-12T08:46:05Z
day: '08'
ddc:
- '000'
department:
- _id: GradSch
- _id: ToHe
doi: 10.46298/lmcs-21(2:2)2025
ec_funded: 1
external_id:
arxiv:
- '2307.06016'
isi:
- '001468887900001'
file:
- access_level: open_access
checksum: 0b4d477bd981379724c35a4de2c176e5
content_type: application/pdf
creator: esarac
date_created: 2025-09-11T12:17:12Z
date_updated: 2025-09-11T12:17:12Z
file_id: '20343'
file_name: 2307.06016.pdf
file_size: 709584
relation: main_file
success: 1
file_date_updated: 2025-09-11T12:17:12Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Logical Methods in Computer Science
publication_identifier:
eissn:
- 1860-5974
publication_status: published
publisher: EPI Sciences
quality_controlled: '1'
related_material:
record:
- id: '13221'
relation: earlier_version
status: public
- id: '20147'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Safety and liveness of quantitative properties and automata
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: publisher
_id: '20147'
abstract:
- lang: eng
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"
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"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Naci E
full_name: Sarac, Naci E
id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425
last_name: Sarac
citation:
ama: Sarac NE. A monitoring-oriented theory and classification of quantitative specifications.
2025. doi:10.15479/AT-ISTA-20147
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.
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.
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.
short: N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative
Specifications, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-07T15:57:57Z
date_published: 2025-08-07T00:00:00Z
date_updated: 2026-08-12T08:46:04Z
day: '07'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/AT-ISTA-20147
doi_confirm: '1'
ec_funded: 1
file:
- access_level: closed
checksum: 0f3015f1db36576a23d8d669afb60b41
content_type: application/x-zip-compressed
creator: esarac
date_created: 2025-08-21T09:40:28Z
date_updated: 2025-09-10T08:19:51Z
file_id: '20200'
file_name: 2025_Sarac_NaciEge_Thesis.zip
file_size: 8884801
relation: source_file
- access_level: open_access
checksum: 332ed2fe61f580641664ec3f05d30f14
content_type: application/pdf
creator: esarac
date_created: 2025-08-21T09:40:34Z
date_updated: 2025-08-21T09:40:34Z
file_id: '20201'
file_name: 2025_Sarac_NaciEge_Thesis.pdf
file_size: 2955584
relation: main_file
success: 1
file_date_updated: 2025-09-10T08:19:51Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '149'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publisher_comment: "In reference to IEEE copyrighted material which is used with permission
in this thesis, the IEEE does not\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'
relation: part_of_dissertation
status: public
- id: '13140'
relation: part_of_dissertation
status: deleted
- id: '19741'
relation: part_of_dissertation
status: public
- id: '19643'
relation: part_of_dissertation
status: deleted
- id: '17634'
relation: part_of_dissertation
status: public
- id: '13221'
relation: part_of_dissertation
status: public
- id: '9356'
relation: part_of_dissertation
status: public
- id: '20342'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: A monitoring-oriented theory and classification of quantitative specifications
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_type: closed access
_id: '22579'
abstract:
- lang: eng
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."
article_number: '106603'
article_processing_charge: No
article_type: original
author:
- first_name: Hisham
full_name: Eldardiry, Hisham
last_name: Eldardiry
- first_name: Shanti Shwarup
full_name: Mahto, Shanti Shwarup
last_name: Mahto
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Stefano
full_name: Galelli, Stefano
last_name: Galelli
citation:
ama: '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'
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'
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.'
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.'
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.'
short: H. Eldardiry, S.S. Mahto, S. Fatichi, S. Galelli, Environmental Modelling
& Software 193 (2025).
das_tickbox: '1'
date_created: 2026-07-27T12:30:25Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-08-12T09:07:29Z
day: '01'
doi: 10.1016/j.envsoft.2025.106603
extern: '1'
intvolume: ' 193'
keyword:
- VIC hydrologic model
- Mekong river
- Large-scale hydrology
- Water resources management
- Reservoir operations
- Remote sensing
language:
- iso: eng
month: '09'
oa_version: None
publication: Environmental Modelling & Software
publication_identifier:
eissn:
- 1873-6726
issn:
- 1364-8152
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'VIC-Res Mekong: An open-source hydrological-water management model for the
Mekong River basin'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 193
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22586'
abstract:
- lang: eng
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.
article_number: '98'
article_processing_charge: No
article_type: original
author:
- first_name: Mengzhu
full_name: Chen, Mengzhu
last_name: Chen
- first_name: Shanti Shwarup
full_name: Mahto, Shanti Shwarup
last_name: Mahto
- first_name: Xiaogang
full_name: He, Xiaogang
last_name: He
- first_name: Changhyun
full_name: Jun, Changhyun
last_name: Jun
- first_name: Athanasios
full_name: Paschalis, Athanasios
last_name: Paschalis
- first_name: Nadav
full_name: Peleg, Nadav
last_name: Peleg
- first_name: Giuseppe
full_name: Mascaro, Giuseppe
last_name: Mascaro
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
citation:
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'
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'
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.'
ieee: 'M. Chen et al., “Record-breaking rainfall: a stochastic approach for
its prediction,” npj Natural Hazards, vol. 2. Springer Nature, 2025.'
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.'
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).
das_tickbox: '1'
date_created: 2026-07-27T12:30:25Z
date_published: 2025-10-29T00:00:00Z
date_updated: 2026-08-12T08:59:35Z
day: '29'
doi: 10.1038/s44304-025-00148-6
extern: '1'
intvolume: ' 2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s44304-025-00148-6
month: '10'
oa: 1
oa_version: Published Version
publication: npj Natural Hazards
publication_identifier:
eissn:
- 2948-2100
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Record-breaking rainfall: a stochastic approach for its prediction'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 2
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19701'
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.'
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).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Pieter Rein Ten
full_name: Wolde, Pieter Rein Ten
last_name: Wolde
citation:
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
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.
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.
ista: Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks.
Annual Review of Biophysics. 54, 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.
short: G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.
corr_author: '1'
date_created: 2025-05-18T22:02:50Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-08-12T09:25:42Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1146/annurev-biophys-060524-102720
external_id:
isi:
- '001488641500013'
pmid:
- '39929539'
file:
- access_level: open_access
checksum: 9ab623b2bc45dcd5fdd2c9577ea8ae9f
content_type: application/pdf
creator: dernst
date_created: 2025-05-19T07:55:51Z
date_updated: 2025-05-19T07:55:51Z
file_id: '19710'
file_name: 2025_AnnualReviewBiophysics_Tkacik.pdf
file_size: 317925
relation: main_file
success: 1
file_date_updated: 2025-05-19T07:55:51Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 249-274
pmid: 1
project:
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information processing in biochemical networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20048'
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.'
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.
article_number: dev204261
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yuuta
full_name: Moriyama, Yuuta
id: addc9b8c-67a0-11f0-b374-a2e094825470
last_name: Moriyama
orcid: 0000-0002-2853-8051
- first_name: Toshiyuki
full_name: Mitsui, Toshiyuki
last_name: Mitsui
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
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.
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.
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.
short: Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).
corr_author: '1'
date_created: 2025-07-21T08:10:32Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2026-08-12T10:01:31Z
day: '27'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.204261
external_id:
isi:
- '001525252300001'
pmid:
- '40576478'
file:
- access_level: open_access
checksum: 808d8aa28df79d23fb661838d1fdc1be
content_type: application/pdf
creator: dernst
date_created: 2025-07-23T08:43:01Z
date_updated: 2025-07-23T08:43:01Z
file_id: '20070'
file_name: 2025_Development_Moriyama.pdf
file_size: 25935563
relation: main_file
success: 1
file_date_updated: 2025-07-23T08:43:01Z
has_accepted_license: '1'
intvolume: ' 152'
isi: 1
issue: '12'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hoxb genes determine the timing of cell ingression by regulating cell surface
fluctuations during zebrafish gastrulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 152
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21343'
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.'
acknowledgement: While working on this paper, the first author was supported by a
FWF grant (DOI 10.55776/P36278).
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Yik Tung
full_name: Chan, Yik Tung
id: c4c0afc8-9262-11ed-9231-d8b0bc743af1
last_name: Chan
orcid: 0000-0001-8467-4106
citation:
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
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
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.
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.
ista: Browning TD, Chan S. 2025. Solubility of a resultant equation and applications.
Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.
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.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-02-22T23:01:36Z
date_published: 2025-10-21T00:00:00Z
date_updated: 2026-08-12T11:17:50Z
day: '21'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.5802/jep.320
external_id:
arxiv:
- '2411.09264'
file:
- access_level: open_access
checksum: 828577ea48ac6109d3e9dd1aeddd45c4
content_type: application/pdf
creator: dernst
date_created: 2026-02-24T07:56:34Z
date_updated: 2026-02-24T07:56:34Z
file_id: '21356'
file_name: 2025_JEP_Browning.pdf
file_size: 1003689
relation: main_file
success: 1
file_date_updated: 2026-02-24T07:56:34Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1677-1691
project:
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
publication: Journal de l'Ecole Polytechnique - Mathematiques
publication_identifier:
eissn:
- 2270-518X
issn:
- 2429-7100
publication_status: published
publisher: Ecole Polytechnique
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Solubility of a resultant equation and applications
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20249'
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.
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)."
article_number: '81'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Florian Alexander
full_name: Wilsch, Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
citation:
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'
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.'
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.'
ista: 'Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics
and numerics. Selecta Mathematica New Series. 31(4), 81.'
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.'
short: T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).
corr_author: '1'
das_tickbox: '1'
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.
date_created: 2025-08-31T22:01:31Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2026-08-12T12:15:32Z
day: '01'
ddc:
- '500'
department:
- _id: TiBr
doi: 10.1007/s00029-025-01074-1
external_id:
arxiv:
- '2407.16315'
isi:
- '001552779800001'
file:
- access_level: open_access
checksum: 89352f1f7e8d2b367ae5f4e9bf9eb1f5
content_type: application/pdf
creator: dernst
date_created: 2025-09-03T06:44:44Z
date_updated: 2025-09-03T06:44:44Z
file_id: '20281'
file_name: 2025_SelectaMathematica_Browning.pdf
file_size: 2484757
relation: main_file
success: 1
file_date_updated: 2025-09-03T06:44:44Z
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 26AEDAB2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P32428
name: New frontiers of the Manin conjecture
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
grant_number: P36278
name: Rational curves via function field analytic number theory
publication: Selecta Mathematica New Series
publication_identifier:
eissn:
- 1420-9020
issn:
- 1022-1824
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/fwilsch/cubicpts
record:
- id: '22234'
relation: research_data
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: 'Integral points on cubic surfaces: heuristics and numerics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2025'
...