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