---
OA_place: publisher
OA_type: hybrid
_id: '19423'
abstract:
- lang: eng
  text: "Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic
    roles in land plants, but its function and transport mechanisms in algae remain
    poorly understood. We therefore aimed to explore the role of IAA in a complex,
    streptophyte algae Chara braunii.\r\nHere, we described novel responses of C.
    braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa
    and CbPINc. We determined their localization in C. braunii using epitope-specific
    antibodies and tested their function in heterologous land plant models. Further,
    using phosphoproteomic analysis, we identified IAA-induced phosphorylation events.\r\nThe
    thallus regeneration assay showed that IAA promotes thallus elongation and side
    branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence
    on the plasma membrane of vegetative and generative cells of C. braunii. However,
    functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin
    transport, whereas CbPINc does not. The IAA is effective in the acceleration of
    cytoplasmic streaming and the phosphorylation of evolutionary conserved targets
    such as homolog of RAF-like kinase.\r\nThese findings suggest that, although canonical
    PIN-mediated auxin transport mechanisms might not be fully conserved in Chara,
    IAA is involved in morphogenesis and fast signaling processes."
acknowledgement: 'This work was supported by funding from the Czech Science Foundation
  project no. 20-13587S to JP and SV, Charles University Grant Agency projects no.
  289523 to KK and no. 393422 to VS, a DOC fellowship of the Austrian Academy of Sciences
  to AS, and the Austrian Science Fund (FWF): I 6123-B to JF. The authors acknowledge
  the Imaging Facility of the Institute of Experimental Botany AS CR supported by
  the MEYS CR (LM2023050 Czech-BioImaging), the Czech Academy of Sciences and IEB
  AS CR, and Viničná Microscopy Core Facility cofinanced by the Czech-BioImaging large
  RI project LM2023050. Computational resources were provided by the e-INFRA CZ project
  (ID:90254), supported by the MEYS CR. The authors would like to thank Ilse Foissner
  and Margit Höftberger for discussing details of immunostaining protocol, Katarzyna
  Retzer and Jan Martinek for help with western blots, Anna Kampová for help with
  phosphoproteome sampling, Anja Holzhausen and MadLAnd for providing Chara braunii
  strain S276, and Roman Skokan for valuable discussion. Open access publishing facilitated
  by Univerzita Karlova, as part of the Wiley - CzechELib agreement.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: K
  full_name: Kurtović, K
  last_name: Kurtović
- first_name: S
  full_name: Vosolsobě, S
  last_name: Vosolsobě
- first_name: D
  full_name: Nedvěd, D
  last_name: Nedvěd
- first_name: K
  full_name: Müller, K
  last_name: Müller
- first_name: PI
  full_name: Dobrev, PI
  last_name: Dobrev
- first_name: V
  full_name: Schmidt, V
  last_name: Schmidt
- first_name: P
  full_name: Piszczek, P
  last_name: Piszczek
- first_name: A
  full_name: Kuhn, A
  last_name: Kuhn
- first_name: Adrijana
  full_name: Smoljan, Adrijana
  id: cced8a85-223e-11ed-af04-b0596c55053b
  last_name: Smoljan
- first_name: TJ
  full_name: Fisher, TJ
  last_name: Fisher
- first_name: D
  full_name: Weijers, D
  last_name: Weijers
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: JL
  full_name: Bowman, JL
  last_name: Bowman
- first_name: J
  full_name: Petrášek, J
  last_name: Petrášek
citation:
  ama: Kurtović K, Vosolsobě S, Nedvěd D, et al. The role of indole-3-acetic acid
    and characterization of PIN transporters in complex streptophyte alga Chara braunii.
    <i>New Phytologist</i>. 2025;246(3):1066-1083. doi:<a href="https://doi.org/10.1111/nph.70019">10.1111/nph.70019</a>
  apa: Kurtović, K., Vosolsobě, S., Nedvěd, D., Müller, K., Dobrev, P., Schmidt, V.,
    … Petrášek, J. (2025). The role of indole-3-acetic acid and characterization of
    PIN transporters in complex streptophyte alga Chara braunii. <i>New Phytologist</i>.
    Wiley. <a href="https://doi.org/10.1111/nph.70019">https://doi.org/10.1111/nph.70019</a>
  chicago: Kurtović, K, S Vosolsobě, D Nedvěd, K Müller, PI Dobrev, V Schmidt, P Piszczek,
    et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters
    in Complex Streptophyte Alga Chara Braunii.” <i>New Phytologist</i>. Wiley, 2025.
    <a href="https://doi.org/10.1111/nph.70019">https://doi.org/10.1111/nph.70019</a>.
  ieee: K. Kurtović <i>et al.</i>, “The role of indole-3-acetic acid and characterization
    of PIN transporters in complex streptophyte alga Chara braunii,” <i>New Phytologist</i>,
    vol. 246, no. 3. Wiley, pp. 1066–1083, 2025.
  ista: Kurtović K, Vosolsobě S, Nedvěd D, Müller K, Dobrev P, Schmidt V, Piszczek
    P, Kuhn A, Smoljan A, Fisher T, Weijers D, Friml J, Bowman J, Petrášek J. 2025.
    The role of indole-3-acetic acid and characterization of PIN transporters in complex
    streptophyte alga Chara braunii. New Phytologist. 246(3), 1066–1083.
  mla: Kurtović, K., et al. “The Role of Indole-3-Acetic Acid and Characterization
    of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” <i>New Phytologist</i>,
    vol. 246, no. 3, Wiley, 2025, pp. 1066–83, doi:<a href="https://doi.org/10.1111/nph.70019">10.1111/nph.70019</a>.
  short: K. Kurtović, S. Vosolsobě, D. Nedvěd, K. Müller, P. Dobrev, V. Schmidt, P.
    Piszczek, A. Kuhn, A. Smoljan, T. Fisher, D. Weijers, J. Friml, J. Bowman, J.
    Petrášek, New Phytologist 246 (2025) 1066–1083.
date_created: 2025-03-19T09:45:11Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-09-30T11:11:18Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.70019
external_id:
  isi:
  - '001438711600001'
  pmid:
  - '40047465'
file:
- access_level: open_access
  checksum: 861c9bf47e7a7766ed03e6d85bd4f6dc
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-16T08:03:36Z
  date_updated: 2025-04-16T08:03:36Z
  file_id: '19571'
  file_name: 2025_NewPhytologist_Kurtovic.pdf
  file_size: 12841729
  relation: main_file
  success: 1
file_date_updated: 2025-04-16T08:03:36Z
has_accepted_license: '1'
intvolume: '       246'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1066-1083
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
  grant_number: I06123
  name: Peptide receptors for auxin canalization in Arabidopsis
publication: New Phytologist
publication_identifier:
  issn:
  - 1469-8137
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of indole-3-acetic acid and characterization of PIN transporters in
  complex streptophyte alga Chara braunii
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 246
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19433'
abstract:
- lang: eng
  text: An ordered r-matching is an r-uniform hypergraph matching equipped with an
    ordering on its vertices. These objects can be viewed as natural generalisations
    of r-dimensional orders. The theory of ordered 2-matchings is well developed and
    has connections and applications to extremal and enumerative combinatorics, probability
    and geometry. On the other hand, in the case  r≥3 much less is known, largely
    due to a lack of powerful bijective tools. Recently, Dudek, Grytczuk and Ruciński
    made some first steps towards a general theory of ordered r-matchings, and in
    this paper we substantially improve several of their results and introduce some
    new directions of study. Many intriguing open questions remain.
acknowledgement: We would like to thank Timo Seppäläinen for some illuminating discussion
  about random high-dimensional orders and for bringing our attention to [59]. We
  would also like to thank the referees for helpful feedback. Michael Anastos is supported
  by the European Union’s Horizon 2020 research and innovation programme under the
  Marie Skłodowska-Curie grant agreement No. 101034413. Matthew Kwan is supported
  by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777, also funded by the European Union.
  Zhihan Jin and Benny Sudakov are supported by SNSF grant 200021-228014.
article_number: e55
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Michael
  full_name: Anastos, Michael
  id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
  last_name: Anastos
- first_name: Zhihan
  full_name: Jin, Zhihan
  last_name: Jin
- first_name: Matthew Alan
  full_name: Kwan, Matthew Alan
  id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
  last_name: Kwan
  orcid: 0000-0002-4003-7567
- first_name: Benny
  full_name: Sudakov, Benny
  last_name: Sudakov
citation:
  ama: Anastos M, Jin Z, Kwan MA, Sudakov B. Extremal, enumerative and probabilistic
    results on ordered hypergraph matchings. <i>Forum of Mathematics, Sigma</i>. 2025;13.
    doi:<a href="https://doi.org/10.1017/fms.2024.144">10.1017/fms.2024.144</a>
  apa: Anastos, M., Jin, Z., Kwan, M. A., &#38; Sudakov, B. (2025). Extremal, enumerative
    and probabilistic results on ordered hypergraph matchings. <i>Forum of Mathematics,
    Sigma</i>. Cambridge University Press. <a href="https://doi.org/10.1017/fms.2024.144">https://doi.org/10.1017/fms.2024.144</a>
  chicago: Anastos, Michael, Zhihan Jin, Matthew Alan Kwan, and Benny Sudakov. “Extremal,
    Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” <i>Forum
    of Mathematics, Sigma</i>. Cambridge University Press, 2025. <a href="https://doi.org/10.1017/fms.2024.144">https://doi.org/10.1017/fms.2024.144</a>.
  ieee: M. Anastos, Z. Jin, M. A. Kwan, and B. Sudakov, “Extremal, enumerative and
    probabilistic results on ordered hypergraph matchings,” <i>Forum of Mathematics,
    Sigma</i>, vol. 13. Cambridge University Press, 2025.
  ista: Anastos M, Jin Z, Kwan MA, Sudakov B. 2025. Extremal, enumerative and probabilistic
    results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 13, e55.
  mla: Anastos, Michael, et al. “Extremal, Enumerative and Probabilistic Results on
    Ordered Hypergraph Matchings.” <i>Forum of Mathematics, Sigma</i>, vol. 13, e55,
    Cambridge University Press, 2025, doi:<a href="https://doi.org/10.1017/fms.2024.144">10.1017/fms.2024.144</a>.
  short: M. Anastos, Z. Jin, M.A. Kwan, B. Sudakov, Forum of Mathematics, Sigma 13
    (2025).
corr_author: '1'
date_created: 2025-03-20T12:59:14Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2025-09-30T11:18:57Z
day: '14'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1017/fms.2024.144
ec_funded: 1
external_id:
  arxiv:
  - '2308.12268'
  isi:
  - '001444429200001'
file:
- access_level: open_access
  checksum: f396270ad78c1ed67095c8e5a66fca26
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-03T11:24:35Z
  date_updated: 2025-04-03T11:24:35Z
  file_id: '19468'
  file_name: 2025_ForumMathSigma_Anastos.pdf
  file_size: 630297
  relation: main_file
  success: 1
file_date_updated: 2025-04-03T11:24:35Z
has_accepted_license: '1'
intvolume: '        13'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
  grant_number: '101076777'
  name: Randomness and structure in combinatorics
publication: Forum of Mathematics, Sigma
publication_identifier:
  issn:
  - 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extremal, enumerative and probabilistic results on ordered hypergraph matchings
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19436'
abstract:
- lang: eng
  text: Dynamic DNA methylation represses transposable elements (TEs) and regulates
    gene activity, playing a pivotal role in plant development. Although substantial
    progress has been made in understanding DNA methylation reprogramming during germline
    development in Arabidopsis thaliana, whether similar mechanisms exist in other
    dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes,
    microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing
    (WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming
    compared to Arabidopsis, while distinct patterns were observed in the dynamics
    of global CG and CHG methylation in B. rapa. Differentially methylated region
    (DMR) analysis identified specifically methylated loci in the male sex cells of
    B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis.
    Additionally, we found that the activity and genomic targeting preference of the
    small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline
    development. A subset of long terminal repeat (LTR) TEs were activated, possibly
    due to the dynamic regulation of DNA methylation during male sexual development
    in B. Rapa. These findings provided new insights into the evolution of epigenetic
    reprogramming mechanisms in plants.
acknowledgement: We thank Prof. Ying Li of Nanjing Agricultural University for her
  help in providing seeds of K2 materials. This work was carried out with the support
  of National Natural Science Foundation of China (Grant No. 32070608).
article_number: '16'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jun
  full_name: Zhang, Jun
  last_name: Zhang
- first_name: Di
  full_name: Wu, Di
  last_name: Wu
- first_name: Yating
  full_name: Zhang, Yating
  last_name: Zhang
- first_name: Xiaoqi
  full_name: Feng, Xiaoqi
  id: e0164712-22ee-11ed-b12a-d80fcdf35958
  last_name: Feng
  orcid: 0000-0002-4008-1234
- first_name: Hongbo
  full_name: Gao, Hongbo
  id: 77c2e73a-eabd-11ef-aee9-8093a2ba7a93
  last_name: Gao
citation:
  ama: Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline
    development in Brassica Rapa. <i>Molecular Horticulture</i>. 2025;5. doi:<a href="https://doi.org/10.1186/s43897-024-00137-9">10.1186/s43897-024-00137-9</a>
  apa: Zhang, J., Wu, D., Zhang, Y., Feng, X., &#38; Gao, H. (2025). DNA methylation
    dynamics in male germline development in Brassica Rapa. <i>Molecular Horticulture</i>.
    Springer Nature. <a href="https://doi.org/10.1186/s43897-024-00137-9">https://doi.org/10.1186/s43897-024-00137-9</a>
  chicago: Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation
    Dynamics in Male Germline Development in Brassica Rapa.” <i>Molecular Horticulture</i>.
    Springer Nature, 2025. <a href="https://doi.org/10.1186/s43897-024-00137-9">https://doi.org/10.1186/s43897-024-00137-9</a>.
  ieee: J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics
    in male germline development in Brassica Rapa,” <i>Molecular Horticulture</i>,
    vol. 5. Springer Nature, 2025.
  ista: Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male
    germline development in Brassica Rapa. Molecular Horticulture. 5, 16.
  mla: Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in
    Brassica Rapa.” <i>Molecular Horticulture</i>, vol. 5, 16, Springer Nature, 2025,
    doi:<a href="https://doi.org/10.1186/s43897-024-00137-9">10.1186/s43897-024-00137-9</a>.
  short: J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2025-09-30T11:17:08Z
day: '04'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1186/s43897-024-00137-9
external_id:
  isi:
  - '001436233900001'
  pmid:
  - '40033451'
file:
- access_level: open_access
  checksum: 6d1e0e9b0e1902e4a711f81c5c17a070
  content_type: application/pdf
  creator: dernst
  date_created: 2025-03-25T12:15:32Z
  date_updated: 2025-03-25T12:15:32Z
  file_id: '19460'
  file_name: 2025_MolecularHorticulture_Zhang.pdf
  file_size: 3014980
  relation: main_file
  success: 1
file_date_updated: 2025-03-25T12:15:32Z
has_accepted_license: '1'
intvolume: '         5'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Horticulture
publication_identifier:
  eissn:
  - 2730-9401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics in male germline development in Brassica Rapa
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19437'
abstract:
- lang: eng
  text: We demonstrate the formation of ferroelectric domain-wall polarons in a minimal
    two-dimensional lattice model of electrons interacting with rotating dipoles.
    Along the domain wall, the rotors polarize in opposite directions, causing the
    electron to localize along a particular lattice direction. The rotor-electron
    coupling is identified as the origin of a structural instability in the crystal
    that leads to the domain-wall formation via a symmetry-breaking process. Our results
    provide the first theoretical description of ferroelectric polarons, as discussed
    in the context of soft semiconductors.
acknowledgement: We thank, in alphabetical order, Zhanybek Alpichshev, Cesare Franchini,
  Areg Ghazaryan, Sebastian Maehrlein, and Artem Volosniev for fruitful discussions
  and comments. G. M. K. received funding from the European Union’s Horizon 2020 research
  and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.
  R. A. received funding from the Austrian Academy of Science ÖWA Grant No. PR1029OEAW03.
  M. L. acknowledges support by the European Research Council (ERC) Starting Grant
  No. 801770 (ANGULON).
article_number: '096302'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Florian
  full_name: Kluibenschedl, Florian
  id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
  last_name: Kluibenschedl
- first_name: Georgios
  full_name: Koutentakis, Georgios
  id: d7b23d3a-9e21-11ec-b482-f76739596b95
  last_name: Koutentakis
- first_name: Ragheed
  full_name: Al Hyder, Ragheed
  id: d1c405be-ae15-11ed-8510-ccf53278162e
  last_name: Al Hyder
- first_name: Mikhail
  full_name: Lemeshko, Mikhail
  id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
  last_name: Lemeshko
  orcid: 0000-0002-6990-7802
citation:
  ama: Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. Domain-wall ferroelectric
    polarons in a two-dimensional rotor lattice model. <i>Physical Review Letters</i>.
    2025;134(9). doi:<a href="https://doi.org/10.1103/PhysRevLett.134.096302">10.1103/PhysRevLett.134.096302</a>
  apa: Kluibenschedl, F., Koutentakis, G., Al Hyder, R., &#38; Lemeshko, M. (2025).
    Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. <i>Physical
    Review Letters</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevLett.134.096302">https://doi.org/10.1103/PhysRevLett.134.096302</a>
  chicago: Kluibenschedl, Florian, Georgios Koutentakis, Ragheed Al Hyder, and Mikhail
    Lemeshko. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice
    Model.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href="https://doi.org/10.1103/PhysRevLett.134.096302">https://doi.org/10.1103/PhysRevLett.134.096302</a>.
  ieee: F. Kluibenschedl, G. Koutentakis, R. Al Hyder, and M. Lemeshko, “Domain-wall
    ferroelectric polarons in a two-dimensional rotor lattice model,” <i>Physical
    Review Letters</i>, vol. 134, no. 9. American Physical Society, 2025.
  ista: Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. 2025. Domain-wall
    ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review
    Letters. 134(9), 096302.
  mla: Kluibenschedl, Florian, et al. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional
    Rotor Lattice Model.” <i>Physical Review Letters</i>, vol. 134, no. 9, 096302,
    American Physical Society, 2025, doi:<a href="https://doi.org/10.1103/PhysRevLett.134.096302">10.1103/PhysRevLett.134.096302</a>.
  short: F. Kluibenschedl, G. Koutentakis, R. Al Hyder, M. Lemeshko, Physical Review
    Letters 134 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-07T00:00:00Z
date_updated: 2025-09-30T11:17:58Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.134.096302
ec_funded: 1
external_id:
  arxiv:
  - '2407.19993'
  isi:
  - '001492808800010'
  pmid:
  - '40131090'
file:
- access_level: open_access
  checksum: 1901efd7f95e8fe70cac412f91ea4da3
  content_type: application/pdf
  creator: dernst
  date_created: 2025-03-25T12:37:07Z
  date_updated: 2025-03-25T12:37:07Z
  file_id: '19461'
  file_name: 2025_PhysReviewLetters_Kluibenschedl.pdf
  file_size: 708750
  relation: main_file
  success: 1
file_date_updated: 2025-03-25T12:37:07Z
has_accepted_license: '1'
intvolume: '       134'
isi: 1
issue: '9'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '801770'
  name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 8fa7db46-16d5-11f0-9cad-917600954daf
  grant_number: '12078'
  name: Polarons in Lead Halide Perovskites
publication: Physical Review Letters
publication_identifier:
  eissn:
  - 1079-7114
  issn:
  - 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 134
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19438'
abstract:
- lang: eng
  text: "Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant,
    although less common than single nucleotide polymorphisms (SNPs). Evidence from
    model organisms shows INDELs to be more strongly influenced by purifying selection
    than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic
    processes or to detect divergent selection. Here, we compared INDELs and SNPs
    in the intertidal snail Littorina saxatilis, focussing on hybrid zones between
    ecotypes, in order to test the utility of INDELs in the detection of divergent
    selection. We computed INDEL and SNP site frequency spectra using capture sequencing
    data. We assessed the impact of divergent selection by analyzing allele frequency
    clines across habitat boundaries. We also examined the influence of GC-biased
    gene conversion because it may be confounded with signatures of selection. We
    show evidence that short INDELs are affected more by purifying selection than
    SNPs, but part of the observed site frequency spectra difference can be attributed
    to GC-biased gene conversion. We did not find a difference in the impact of divergent
    selection between short INDELs and SNPs. Short INDELs and SNPs were similarly
    distributed across the genome and so are likely to respond to indirect selection
    in the same way. A few regions likely affected by divergent selection were revealed
    by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers
    helping to identify genomic regions important for adaptation and population divergence."
acknowledgement: "This work was supported by the Natural Environment Research Council
  (NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish
  Research Council VR (2018-03695) and we are also very grateful for the support of
  the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe
  thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback
  and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions.
  R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to
  Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and
  the annotation. The bioinformatic analyses were performed on resources at the University
  of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous
  reviewers for helpful comments on a previous version."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Samuel
  full_name: Perini, Samuel
  last_name: Perini
- first_name: Kerstin
  full_name: Johannesson, Kerstin
  last_name: Johannesson
- first_name: Roger K.
  full_name: Butlin, Roger K.
  last_name: Butlin
- first_name: Anja M
  full_name: Westram, Anja M
  id: 3C147470-F248-11E8-B48F-1D18A9856A87
  last_name: Westram
  orcid: 0000-0003-1050-4969
citation:
  ama: Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers
    of evolutionary processes in hybrid zones. <i>Journal of Evolutionary Biology</i>.
    2025;38(3):367-378. doi:<a href="https://doi.org/10.1093/jeb/voaf002">10.1093/jeb/voaf002</a>
  apa: Perini, S., Johannesson, K., Butlin, R. K., &#38; Westram, A. M. (2025). Short
    INDELs and SNPs as markers of evolutionary processes in hybrid zones. <i>Journal
    of Evolutionary Biology</i>. Oxford University Press. <a href="https://doi.org/10.1093/jeb/voaf002">https://doi.org/10.1093/jeb/voaf002</a>
  chicago: Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram.
    “Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.”
    <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2025. <a href="https://doi.org/10.1093/jeb/voaf002">https://doi.org/10.1093/jeb/voaf002</a>.
  ieee: S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs
    and SNPs as markers of evolutionary processes in hybrid zones,” <i>Journal of
    Evolutionary Biology</i>, vol. 38, no. 3. Oxford University Press, pp. 367–378,
    2025.
  ista: Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs
    as markers of evolutionary processes in hybrid zones. Journal of Evolutionary
    Biology. 38(3), 367–378.
  mla: Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes
    in Hybrid Zones.” <i>Journal of Evolutionary Biology</i>, vol. 38, no. 3, Oxford
    University Press, 2025, pp. 367–78, doi:<a href="https://doi.org/10.1093/jeb/voaf002">10.1093/jeb/voaf002</a>.
  short: S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary
    Biology 38 (2025) 367–378.
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:19:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voaf002
external_id:
  isi:
  - '001415267900001'
  pmid:
  - '39803902'
file:
- access_level: open_access
  checksum: 01408e626a4131bfec5ffc70b0af9129
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-03T11:53:06Z
  date_updated: 2025-04-03T11:53:06Z
  file_id: '19469'
  file_name: 2025_JourEvolBiology_Perini.pdf
  file_size: 12826085
  relation: main_file
  success: 1
file_date_updated: 2025-04-03T11:53:06Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 367-378
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
  eissn:
  - 1420-9101
  issn:
  - 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19439'
abstract:
- lang: eng
  text: "White dwarfs (WDs) are the most abundant compact objects, and recent surveys
    have suggested that over a third of WDs in accreting binaries host a strong (B
    \ ≳ 1 MG) magnetic field. However, the origin and evolution of WD magnetism remain
    under debate. Two WD pulsars, AR Sco and J191213.72–441045.1 (J1912), have been
    found, which are non-accreting binaries hosting rapidly spinning (1.97 minutes
    and 5.30 minutes, respectively) magnetic WDs. The WD in AR Sco is slowing down
    on a (math formular) yr timescale. It is believed they will eventually become
    polars, accreting systems in which a magnetic WD (B  ≈ 10−240 MG) accretes from
    a Roche lobe-filling donor spinning in sync with the orbit (≳78 minutes). Here,
    we present multiwavelength data and analysis of Gaia22ayj, which outbursted in
    2022 March. We find that Gaia22ayj is a magnetic accreting WD that is rapidly
    spinning down (math formular\r\n yr) like WD pulsars, but shows clear evidence
    of accretion, like polars. Strong linear polarization (40%) is detected in Gaia22ayj;
    such high levels have only been seen in the WD pulsar AR Sco and demonstrate the
    WD is magnetic. High speed photometry reveals a 9.36 minutes period accompanying
    a high amplitude (∼2 mag) modulation. We associate this with a WD spin or spin–orbit
    beat period, not an orbital period as was previously suggested. Fast (60 s) optical
    spectroscopy reveals a broad \"hump,\" reminiscent of cyclotron emission in polars,
    between 4000 and 8000 Å. We find an X-ray luminosity of (math formular) in the
    0.3–8 keV energy range, while two very large array radio campaigns resulted in
    a non-detection with a Fr < 15.8 μJy 3σ upper limit. The shared properties of
    both WD pulsars and polars suggest that Gaia22ayj is a missing link between the
    two classes of magnetic WD binaries."
acknowledgement: "We wish to dedicate this work to the memory of our colleague and
  friend Tom Marsh. Tom's enthusiasm to work on this object and rapid efforts to facilitate
  data collection truly made this project possible.\r\n\r\nA.C.R. acknowledges support
  from an NSF Graduate Fellowship. A.C.R. thanks the LSST-DA Data Science Fellowship
  Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation;
  his participation in the program has benefited this work. P.R.-G. acknowledges support
  by the Spanish Agencia Estatal de Investigación del Ministerio de Ciencia e Innovación
  (MCIN/AEI) and the European Regional Development Fund (ERDF) under grant PID2021–124879NB–I00.
  M.R.S. is supported by FONDECYT (grant No. 1221059) and eRO-STEP (SA 2131/15-2 project
  number 414059771). I.P. acknowledges support from a Royal Society University Research
  Fellowship (URF/R1/231496). We thank the referee for feedback that improved the
  clarity of this paper.\r\n\r\nBased on observations made with the Gran Telescopio
  Canarias (GTC), installed at the Spanish Observatorio del Roque de los Muchachos
  of the Instituto de Astrofìsica de Canarias, on the island of La Palma. Based on
  observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope
  at the Palomar Observatory as part of the ZTF project. ZTF is supported by the National
  Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration
  including current partners Caltech, IPAC, the Weizmann Institute of Science, the
  Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches
  Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan,
  the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore
  National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern
  University and former partners the University of Washington, Los Alamos National
  Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted
  by COO, IPAC, and UW.\r\n\r\nSome of the data presented herein were obtained at
  Keck Observatory, which is a private 501(c)3 non-profit organization operated as
  a scientific partnership among the California Institute of Technology, the University
  of California, and the National Aeronautics and Space Administration. The Observatory
  was made possible by the generous financial support of the W. M. Keck Foundation.
  The authors wish to recognize and acknowledge the very significant cultural role
  and reverence that the summit of Maunakea has always had within the Native Hawaiian
  community. We are most fortunate to have the opportunity to conduct observations
  from this mountain. We are also grateful to the staff of Palomar Observatory for
  their assistance in carrying out observations used in this work.\r\n\r\nPartly based
  on observations made with the NOT, owned in collaboration by the University of Turku
  and Aarhus University, and operated jointly by Aarhus University, the University
  of Turku and the University of Oslo, representing Denmark, Finland and Norway, the
  University of Iceland and Stockholm University at the Observatorio del Roque de
  los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias. The
  data presented here were obtained with ALFOSC, which is provided by the Instituto
  de Astrofisica de Andalucia (IAA) under a joint agreement with the University of
  Copenhagen and NOT. The observation with the SALT was obtained under program 2021-2-LSP-001
  (PI: D. Buckley). Polish participation in SALT is funded by grant No. MEiN nr 2021/WK/01.
  D.A.H.B. acknowledges support from the National Research Foundation.\r\n\r\nThis
  work presents results from the European Space Agency (ESA) space mission Gaia. Gaia
  data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC).
  Funding for the DPAC is provided by national institutions, in particular the institutions
  participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website
  is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia.
  This work made use of data supplied by the UK Swift Science Data Centre at the University
  of Leicester\r\n\r\nE.C.B. and J.K. acknowledge support from the DIRAC Institute
  in the Department of Astronomy at the University of Washington. The DIRAC Institute
  is supported through generous gifts from the Charles and Lisa Simonyi Fund for Arts
  and Sciences, and the Washington Research Foundation."
article_number: '024202'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Antonio C.
  full_name: Rodriguez, Antonio C.
  last_name: Rodriguez
- first_name: Kareem
  full_name: El-Badry, Kareem
  last_name: El-Badry
- first_name: Pasi
  full_name: Hakala, Pasi
  last_name: Hakala
- first_name: Pablo
  full_name: Rodríguez-Gil, Pablo
  last_name: Rodríguez-Gil
- first_name: Tong
  full_name: Bao, Tong
  last_name: Bao
- first_name: Ilkham
  full_name: Galiullin, Ilkham
  last_name: Galiullin
- first_name: Jacob A.
  full_name: Kurlander, Jacob A.
  last_name: Kurlander
- first_name: Casey J.
  full_name: Law, Casey J.
  last_name: Law
- first_name: Ingrid
  full_name: Pelisoli, Ingrid
  last_name: Pelisoli
- first_name: Matthias R.
  full_name: Schreiber, Matthias R.
  last_name: Schreiber
- first_name: Kevin
  full_name: Burdge, Kevin
  last_name: Burdge
- first_name: Ilaria
  full_name: Caiazzo, Ilaria
  id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
  last_name: Caiazzo
  orcid: 0000-0002-4770-5388
- first_name: Jan Van
  full_name: Roestel, Jan Van
  last_name: Roestel
- first_name: Paula
  full_name: Szkody, Paula
  last_name: Szkody
- first_name: Andrew J.
  full_name: Drake, Andrew J.
  last_name: Drake
- first_name: David A.H.
  full_name: Buckley, David A.H.
  last_name: Buckley
- first_name: Stephen B.
  full_name: Potter, Stephen B.
  last_name: Potter
- first_name: Boris
  full_name: Gaensicke, Boris
  last_name: Gaensicke
- first_name: Kaya
  full_name: Mori, Kaya
  last_name: Mori
- first_name: Eric C.
  full_name: Bellm, Eric C.
  last_name: Bellm
- first_name: Shrinivas R.
  full_name: Kulkarni, Shrinivas R.
  last_name: Kulkarni
- first_name: Thomas A.
  full_name: Prince, Thomas A.
  last_name: Prince
- first_name: Matthew
  full_name: Graham, Matthew
  last_name: Graham
- first_name: Mansi M.
  full_name: Kasliwal, Mansi M.
  last_name: Kasliwal
- first_name: Sam
  full_name: Rose, Sam
  last_name: Rose
- first_name: Yashvi
  full_name: Sharma, Yashvi
  last_name: Sharma
- first_name: Tomás
  full_name: Ahumada, Tomás
  last_name: Ahumada
- first_name: Shreya
  full_name: Anand, Shreya
  last_name: Anand
- first_name: Akke
  full_name: Viitanen, Akke
  last_name: Viitanen
- first_name: Avery
  full_name: Wold, Avery
  last_name: Wold
- first_name: Tracy X.
  full_name: Chen, Tracy X.
  last_name: Chen
- first_name: Reed
  full_name: Riddle, Reed
  last_name: Riddle
- first_name: Roger
  full_name: Smith, Roger
  last_name: Smith
citation:
  ama: 'Rodriguez AC, El-Badry K, Hakala P, et al. A link between White Dwarf pulsars
    and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj.
    <i>Publications of the Astronomical Society of the Pacific</i>. 2025;137(2). doi:<a
    href="https://doi.org/10.1088/1538-3873/adb0f1">10.1088/1538-3873/adb0f1</a>'
  apa: 'Rodriguez, A. C., El-Badry, K., Hakala, P., Rodríguez-Gil, P., Bao, T., Galiullin,
    I., … Smith, R. (2025). A link between White Dwarf pulsars and polars: Multiwavelength
    observations of the 9.36-minute period variable Gaia22ayj. <i>Publications of
    the Astronomical Society of the Pacific</i>. IOP Publishing. <a href="https://doi.org/10.1088/1538-3873/adb0f1">https://doi.org/10.1088/1538-3873/adb0f1</a>'
  chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Pasi Hakala, Pablo Rodríguez-Gil,
    Tong Bao, Ilkham Galiullin, Jacob A. Kurlander, et al. “A Link between White Dwarf
    Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable
    Gaia22ayj.” <i>Publications of the Astronomical Society of the Pacific</i>. IOP
    Publishing, 2025. <a href="https://doi.org/10.1088/1538-3873/adb0f1">https://doi.org/10.1088/1538-3873/adb0f1</a>.'
  ieee: 'A. C. Rodriguez <i>et al.</i>, “A link between White Dwarf pulsars and polars:
    Multiwavelength observations of the 9.36-minute period variable Gaia22ayj,” <i>Publications
    of the Astronomical Society of the Pacific</i>, vol. 137, no. 2. IOP Publishing,
    2025.'
  ista: 'Rodriguez AC, El-Badry K, Hakala P, Rodríguez-Gil P, Bao T, Galiullin I,
    Kurlander JA, Law CJ, Pelisoli I, Schreiber MR, Burdge K, Caiazzo I, Roestel JV,
    Szkody P, Drake AJ, Buckley DAH, Potter SB, Gaensicke B, Mori K, Bellm EC, Kulkarni
    SR, Prince TA, Graham M, Kasliwal MM, Rose S, Sharma Y, Ahumada T, Anand S, Viitanen
    A, Wold A, Chen TX, Riddle R, Smith R. 2025. A link between White Dwarf pulsars
    and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj.
    Publications of the Astronomical Society of the Pacific. 137(2), 024202.'
  mla: 'Rodriguez, Antonio C., et al. “A Link between White Dwarf Pulsars and Polars:
    Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” <i>Publications
    of the Astronomical Society of the Pacific</i>, vol. 137, no. 2, 024202, IOP Publishing,
    2025, doi:<a href="https://doi.org/10.1088/1538-3873/adb0f1">10.1088/1538-3873/adb0f1</a>.'
  short: A.C. Rodriguez, K. El-Badry, P. Hakala, P. Rodríguez-Gil, T. Bao, I. Galiullin,
    J.A. Kurlander, C.J. Law, I. Pelisoli, M.R. Schreiber, K. Burdge, I. Caiazzo,
    J.V. Roestel, P. Szkody, A.J. Drake, D.A.H. Buckley, S.B. Potter, B. Gaensicke,
    K. Mori, E.C. Bellm, S.R. Kulkarni, T.A. Prince, M. Graham, M.M. Kasliwal, S.
    Rose, Y. Sharma, T. Ahumada, S. Anand, A. Viitanen, A. Wold, T.X. Chen, R. Riddle,
    R. Smith, Publications of the Astronomical Society of the Pacific 137 (2025).
date_created: 2025-03-23T23:01:26Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-09-30T11:15:10Z
day: '01'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1088/1538-3873/adb0f1
external_id:
  arxiv:
  - '2501.01490'
  isi:
  - '001427877700001'
file:
- access_level: open_access
  checksum: 42d5aa504479c3fdf2a10165a9e3319f
  content_type: application/pdf
  creator: dernst
  date_created: 2025-03-25T10:01:24Z
  date_updated: 2025-03-25T10:01:24Z
  file_id: '19455'
  file_name: 2025_PubAstronomSocPacific_Rodriguez.pdf
  file_size: 3291933
  relation: main_file
  success: 1
file_date_updated: 2025-03-25T10:01:24Z
has_accepted_license: '1'
intvolume: '       137'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
  issn:
  - 0004-6280
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A link between White Dwarf pulsars and polars: Multiwavelength observations
  of the 9.36-minute period variable Gaia22ayj'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 137
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19440'
abstract:
- lang: eng
  text: Let μ(G) denote the minimum number of edges whose addition to G results in
    a Hamiltonian graph, and let μ^(G) denote the minimum number of edges whose addition
    to G results in a pancyclic graph. We study the distributions of μ(G),μ^(G) in
    the context of binomial random graphs. Letting d=d(n):=n⋅p, we prove that there
    exists a function f:R+→[0,1] of order f(d)=12de−d+e−d+O(d6e−3d) such that, if
    G∼G(n,p) with 20≤d(n)≤0.4logn, then with high probability μ(G)=(1+o(1))⋅f(d)⋅n.
    Let ni(G) denote the number of degree i vertices in G. A trivial lower bound on
    μ(G) is given by the expression n0(G)+⌈12n1(G)⌉. In the denser regime of random
    graphs, we show that if np−13logn−2loglogn→∞ and G∼G(n,p) then, with high probability,
    μ(G)=n0(G)+⌈12n1(G)⌉. For completion to pancyclicity, we show that if G∼G(n,p)
    and np≥20 then, with high probability, μ^(G)=μ(G). Finally, we present a polynomial
    time algorithm such that, if G∼G(n,p) and np≥20, then, with high probability,
    the algorithm returns a set of edges of size μ(G) whose addition to G results
    in a pancyclic (and therefore also Hamiltonian) graph.
acknowledgement: The authors would like to express their thanks to the referees of
  the article for their valuable input towards improving the presentation of our result.
  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.
article_number: e21286
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Yahav
  full_name: Alon, Yahav
  last_name: Alon
- first_name: Michael
  full_name: Anastos, Michael
  id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
  last_name: Anastos
citation:
  ama: Alon Y, Anastos M. The completion numbers of hamiltonicity and pancyclicity
    in random graphs. <i>Random Structures and Algorithms</i>. 2025;66(2). doi:<a
    href="https://doi.org/10.1002/rsa.21286">10.1002/rsa.21286</a>
  apa: Alon, Y., &#38; Anastos, M. (2025). The completion numbers of hamiltonicity
    and pancyclicity in random graphs. <i>Random Structures and Algorithms</i>. Wiley.
    <a href="https://doi.org/10.1002/rsa.21286">https://doi.org/10.1002/rsa.21286</a>
  chicago: Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity
    and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>. Wiley,
    2025. <a href="https://doi.org/10.1002/rsa.21286">https://doi.org/10.1002/rsa.21286</a>.
  ieee: Y. Alon and M. Anastos, “The completion numbers of hamiltonicity and pancyclicity
    in random graphs,” <i>Random Structures and Algorithms</i>, vol. 66, no. 2. Wiley,
    2025.
  ista: Alon Y, Anastos M. 2025. The completion numbers of hamiltonicity and pancyclicity
    in random graphs. Random Structures and Algorithms. 66(2), e21286.
  mla: Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity
    and Pancyclicity in Random Graphs.” <i>Random Structures and Algorithms</i>, vol.
    66, no. 2, e21286, Wiley, 2025, doi:<a href="https://doi.org/10.1002/rsa.21286">10.1002/rsa.21286</a>.
  short: Y. Alon, M. Anastos, Random Structures and Algorithms 66 (2025).
date_created: 2025-03-23T23:01:26Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:15:41Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1002/rsa.21286
ec_funded: 1
external_id:
  arxiv:
  - '2304.03710'
  isi:
  - '001420226800001'
file:
- access_level: open_access
  checksum: 6067747e805fa356d560dc45f2a89918
  content_type: application/pdf
  creator: dernst
  date_created: 2025-03-25T11:46:27Z
  date_updated: 2025-03-25T11:46:27Z
  file_id: '19459'
  file_name: 2025_RandomStruc_Alon.pdf
  file_size: 549236
  relation: main_file
  success: 1
file_date_updated: 2025-03-25T11:46:27Z
has_accepted_license: '1'
intvolume: '        66'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Random Structures and Algorithms
publication_identifier:
  eissn:
  - 1098-2418
  issn:
  - 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The completion numbers of hamiltonicity and pancyclicity in random graphs
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: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 66
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19441'
abstract:
- lang: eng
  text: Catalytic microswimmers convert the chemical energy from fuel into motion.
    They sustain chemical gradients and fluid flows that propel them by phoresis.
    This leads to unconventional behavior and collective dynamics, such as self-organization
    into complex structures. Characterizing the nonequilibrium interactions of microswimmers
    is crucial for advancing our understanding of active systems. However, this remains
    a challenge owing to the importance of fluctuations at the microscale and the
    difficulty in disentangling the different contributions to the interactions. Here,
    we show a massive dependence of the nonequilibrium interactions on the shape of
    catalytic microswimmers. We perform tracking experiments at high throughput to
    map interactions between nanocolloidal tracers and dimeric microswimmers of various
    aspect ratios. Our method leverages dual tracers with differing phoretic mobilities
    to quantitatively disentangle phoretic motion from hydrodynamic advection. This
    approach is validated through experiments on single chemically active sites and
    on immobilized catalytic microswimmers. We further investigate the activity-driven
    interactions of free microswimmers and directly measure their phoretic interactions.
    When compared to standard models, our findings highlight the important role of
    osmotic flows for microswimmers near surfaces and reveal an enhanced contribution
    of hydrodynamic advection relative to phoretic motion as the size of the microswimmer
    increases. Our study provides robust measurements of the nonequilibrium interactions
    from catalytic microswimmers and lays the groundwork for a realistic description
    of active systems.
acknowledgement: The authors thank M. Perrin and A. Allard for enlightening discussions.
  This research was funded in whole or in part by the Austrian Science Fund (FWF)
  [10.55776/P35206]. This project has received funding from the European Union’s Horizon
  2020 research and innovation programme under the Marie Sklodowska Curie grant agreement
  No. 886024.
article_processing_charge: No
article_type: original
author:
- first_name: Celso
  full_name: Carrasco, Celso
  last_name: Carrasco
- first_name: Quentin
  full_name: Martinet, Quentin
  id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
  last_name: Martinet
  orcid: 0000-0002-2916-6632
- first_name: Zaiyi
  full_name: Shen, Zaiyi
  last_name: Shen
- first_name: Juho
  full_name: Lintuvuori, Juho
  last_name: Lintuvuori
- first_name: Jérémie A
  full_name: Palacci, Jérémie A
  id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
  last_name: Palacci
  orcid: 0000-0002-7253-9465
- first_name: Antoine
  full_name: Aubret, Antoine
  last_name: Aubret
citation:
  ama: Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. Characterization
    of nonequilibrium interactions of catalytic microswimmers using phoretically responsive
    nanotracers. <i>ACS Nano</i>. 2025;19(11):11133-11145. doi:<a href="https://doi.org/10.1021/acsnano.4c18078">10.1021/acsnano.4c18078</a>
  apa: Carrasco, C., Martinet, Q., Shen, Z., Lintuvuori, J., Palacci, J. A., &#38;
    Aubret, A. (2025). Characterization of nonequilibrium interactions of catalytic
    microswimmers using phoretically responsive nanotracers. <i>ACS Nano</i>. American
    Chemical Society. <a href="https://doi.org/10.1021/acsnano.4c18078">https://doi.org/10.1021/acsnano.4c18078</a>
  chicago: Carrasco, Celso, Quentin Martinet, Zaiyi Shen, Juho Lintuvuori, Jérémie
    A Palacci, and Antoine Aubret. “Characterization of Nonequilibrium Interactions
    of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS
    Nano</i>. American Chemical Society, 2025. <a href="https://doi.org/10.1021/acsnano.4c18078">https://doi.org/10.1021/acsnano.4c18078</a>.
  ieee: C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J. A. Palacci, and A. Aubret,
    “Characterization of nonequilibrium interactions of catalytic microswimmers using
    phoretically responsive nanotracers,” <i>ACS Nano</i>, vol. 19, no. 11. American
    Chemical Society, pp. 11133–11145, 2025.
  ista: Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. 2025.
    Characterization of nonequilibrium interactions of catalytic microswimmers using
    phoretically responsive nanotracers. ACS Nano. 19(11), 11133–11145.
  mla: Carrasco, Celso, et al. “Characterization of Nonequilibrium Interactions of
    Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” <i>ACS Nano</i>,
    vol. 19, no. 11, American Chemical Society, 2025, pp. 11133–45, doi:<a href="https://doi.org/10.1021/acsnano.4c18078">10.1021/acsnano.4c18078</a>.
  short: C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J.A. Palacci, A. Aubret,
    ACS Nano 19 (2025) 11133–11145.
date_created: 2025-03-23T23:01:26Z
date_published: 2025-03-11T00:00:00Z
date_updated: 2025-10-16T10:26:59Z
day: '11'
department:
- _id: JePa
doi: 10.1021/acsnano.4c18078
external_id:
  isi:
  - '001443359300001'
  pmid:
  - '40069094'
intvolume: '        19'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://hal.science/hal-04682818v2
month: '03'
oa: 1
oa_version: Submitted Version
page: 11133-11145
pmid: 1
project:
- _id: eb99c9bb-77a9-11ec-83b8-9f8cffa20a35
  grant_number: P35206
  name: Emergent Behavior in Spinning Active Matter
publication: ACS Nano
publication_identifier:
  eissn:
  - 1936-086X
  issn:
  - 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterization of nonequilibrium interactions of catalytic microswimmers
  using phoretically responsive nanotracers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19442'
abstract:
- lang: eng
  text: "1. Climate change is expected to induce shifts in the composition, structure
    and functioning of Arctic tundra ecosystems. Increases in the frequency and severity
    of tundra fires have the potential to catalyse vegetation transitions with far-reaching
    local, regional and global consequences.\r\n2. We propose that post-fire tundra
    recovery, coupled with climate change, may not necessarily lead to pre-fire conditions.
    Our hypothesis, based on surveys and literature, suggests two climate–fire driven
    trajectories. One trajectory results in increased woody vegetation under low fire
    frequency; the other results in grass dominance under high frequency.\r\n3. Future
    research should address uncertainties regarding possible tundra ecosystem shifts
    linked to fires, using methods that encompass greater temporal and spatial scales
    than previously addressed. More case studies, especially in underrepresented regions
    and ecosystem types, are essential to broaden the empirical basis for forecasts
    and potential fire management strategies.\r\n4. Synthesis. Our review synthesises
    current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems,
    highlighting potential transitions and alternative ecosystem states and their
    implications. We discuss challenges in defining and predicting these trajectories
    as well as future directions."
acknowledgement: We would like to express our sincere gratitude to all the data providers
  who carried out fieldwork in different regions of the Arctic and published their
  data, which we used for our meta-analysis. We recognise the hard work and dedication
  of these individuals, without whom this paper would not have been possible. We are
  grateful to the editor and the anonymous reviewer for their time and valuable feedback
  on this manuscript. We particularly appreciate the detailed and constructive comments
  provided by reviewer Mara Baudena, which significantly strengthened our work. We
  also acknowledge the Indigenous peoples and rural communities of the Arctic, whose
  traditional knowledge, rights, and interests are integral to the stewardship and
  study of these ecosystems. This work was funded in part by the U.S. National Aeronautics
  and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled
  and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Ramona Julia
  full_name: Heim, Ramona Julia
  last_name: Heim
- first_name: Adrian V.
  full_name: Rocha, Adrian V.
  last_name: Rocha
- first_name: Vitalii
  full_name: Zemlianskii, Vitalii
  last_name: Zemlianskii
- first_name: Kirsten
  full_name: Barrett, Kirsten
  last_name: Barrett
- first_name: Helga
  full_name: Bültmann, Helga
  last_name: Bültmann
- first_name: Amy
  full_name: Breen, Amy
  last_name: Breen
- first_name: Gerald Verner
  full_name: Frost, Gerald Verner
  last_name: Frost
- first_name: Teresa Nettleton
  full_name: Hollingsworth, Teresa Nettleton
  last_name: Hollingsworth
- first_name: Randi
  full_name: Jandt, Randi
  last_name: Jandt
- first_name: Maria
  full_name: Kozlova, Maria
  last_name: Kozlova
- first_name: Anastasiya
  full_name: Kurka, Anastasiya
  last_name: Kurka
- first_name: Mark Torre
  full_name: Jorgenson, Mark Torre
  last_name: Jorgenson
- first_name: Simon M.
  full_name: Landhäusser, Simon M.
  last_name: Landhäusser
- first_name: Michael Mark
  full_name: Loranty, Michael Mark
  last_name: Loranty
- first_name: Eric A.
  full_name: Miller, Eric A.
  last_name: Miller
- first_name: Kenji
  full_name: Narita, Kenji
  last_name: Narita
- first_name: Evgeniya
  full_name: Pravdolyubova, Evgeniya
  id: 0b30719b-13f0-11ed-ab2a-94498bc6a278
  last_name: Pravdolyubova
- first_name: Norbert
  full_name: Hölzel, Norbert
  last_name: Hölzel
- first_name: Gabriela
  full_name: Schaepman-Strub, Gabriela
  last_name: Schaepman-Strub
citation:
  ama: Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative
    ecosystem states in a changing climate? <i>Journal of Ecology</i>. 2025;113(5):1042-1056.
    doi:<a href="https://doi.org/10.1111/1365-2745.70022">10.1111/1365-2745.70022</a>
  apa: Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen,
    A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative
    ecosystem states in a changing climate? <i>Journal of Ecology</i>. Wiley. <a href="https://doi.org/10.1111/1365-2745.70022">https://doi.org/10.1111/1365-2745.70022</a>
  chicago: Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett,
    Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems
    under Fire—Alternative Ecosystem States in a Changing Climate?” <i>Journal of
    Ecology</i>. Wiley, 2025. <a href="https://doi.org/10.1111/1365-2745.70022">https://doi.org/10.1111/1365-2745.70022</a>.
  ieee: R. J. Heim <i>et al.</i>, “Arctic tundra ecosystems under fire—Alternative
    ecosystem states in a changing climate?,” <i>Journal of Ecology</i>, vol. 113,
    no. 5. Wiley, pp. 1042–1056, 2025.
  ista: Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV,
    Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty
    MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic
    tundra ecosystems under fire—Alternative ecosystem states in a changing climate?
    Journal of Ecology. 113(5), 1042–1056.
  mla: Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative
    Ecosystem States in a Changing Climate?” <i>Journal of Ecology</i>, vol. 113,
    no. 5, Wiley, 2025, pp. 1042–56, doi:<a href="https://doi.org/10.1111/1365-2745.70022">10.1111/1365-2745.70022</a>.
  short: R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen,
    G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson,
    S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel,
    G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.
date_created: 2025-03-23T23:01:27Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-12-30T08:09:47Z
day: '01'
ddc:
- '550'
- '570'
department:
- _id: NiBa
doi: 10.1111/1365-2745.70022
external_id:
  isi:
  - '001443422900001'
file:
- access_level: open_access
  checksum: e2785ae265e211b4dc7fc9c5b7744948
  content_type: application/pdf
  creator: dernst
  date_created: 2025-12-30T08:08:18Z
  date_updated: 2025-12-30T08:08:18Z
  file_id: '20890'
  file_name: 2025_JournEcology_Heim.pdf
  file_size: 2662766
  relation: main_file
  success: 1
file_date_updated: 2025-12-30T08:08:18Z
has_accepted_license: '1'
intvolume: '       113'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1042-1056
publication: Journal of Ecology
publication_identifier:
  eissn:
  - 1365-2745
  issn:
  - 0022-0477
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing
  climate?
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19443'
abstract:
- lang: eng
  text: In cryo-electron microscopy, accurate particle localization and classification
    are imperative. Recent deep learning solutions, though successful, require extensive
    training datasets. The protracted generation time of physics-based models, often
    employed to produce these datasets, limits their broad applicability. We introduce
    FakET, a method based on neural style transfer, capable of simulating the forward
    operator of any cryo transmission electron microscope. It can be used to adapt
    a synthetic training dataset according to reference data producing high-quality
    simulated micrographs or tilt-series. To assess the quality of our generated data,
    we used it to train a state-of-the-art localization and classification architecture
    and compared its performance with a counterpart trained on benchmark data. Remarkably,
    our technique matches the performance, boosts data generation speed 750x, uses
    33x less memory, and scales well to typical transmission electron microscope detector
    sizes. It leverages GPU acceleration and parallel processing. The source code
    is available at https://github.com/paloha/faket/.
acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We
  thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins
  and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for
  helpful discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pavol
  full_name: Harar, Pavol
  id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
  last_name: Harar
  orcid: 0000-0001-5206-1794
- first_name: Lukas
  full_name: Herrmann, Lukas
  last_name: Herrmann
- first_name: Philipp
  full_name: Grohs, Philipp
  last_name: Grohs
- first_name: David
  full_name: Haselbach, David
  last_name: Haselbach
citation:
  ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron
    tomograms with neural style transfer. <i>Structure</i>. 2025;33(4):820-827.e4.
    doi:<a href="https://doi.org/10.1016/j.str.2025.01.020">10.1016/j.str.2025.01.020</a>'
  apa: 'Harar, P., Herrmann, L., Grohs, P., &#38; Haselbach, D. (2025). FakET: Simulating
    cryo-electron tomograms with neural style transfer. <i>Structure</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.str.2025.01.020">https://doi.org/10.1016/j.str.2025.01.020</a>'
  chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET:
    Simulating Cryo-Electron Tomograms with Neural Style Transfer.” <i>Structure</i>.
    Elsevier, 2025. <a href="https://doi.org/10.1016/j.str.2025.01.020">https://doi.org/10.1016/j.str.2025.01.020</a>.'
  ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron
    tomograms with neural style transfer,” <i>Structure</i>, vol. 33, no. 4. Elsevier,
    p. 820–827.e4, 2025.'
  ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron
    tomograms with neural style transfer. Structure. 33(4), 820–827.e4.'
  mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural
    Style Transfer.” <i>Structure</i>, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4,
    doi:<a href="https://doi.org/10.1016/j.str.2025.01.020">10.1016/j.str.2025.01.020</a>.'
  short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.
corr_author: '1'
date_created: 2025-03-23T23:01:27Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2025-09-30T11:13:02Z
day: '03'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.str.2025.01.020
external_id:
  isi:
  - '001463196100001'
  pmid:
  - '39947174'
file:
- access_level: open_access
  checksum: f346bc357a66a88cca3d0eb95793fb73
  content_type: application/pdf
  creator: dernst
  date_created: 2025-08-05T12:15:13Z
  date_updated: 2025-08-05T12:15:13Z
  file_id: '20130'
  file_name: 2025_Structure_Harar.pdf
  file_size: 4367530
  relation: main_file
  success: 1
file_date_updated: 2025-08-05T12:15:13Z
has_accepted_license: '1'
intvolume: '        33'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 820-827.e4
pmid: 1
publication: Structure
publication_identifier:
  eissn:
  - 1878-4186
  issn:
  - 0969-2126
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/paloha/faket/
scopus_import: '1'
status: public
title: 'FakET: Simulating cryo-electron tomograms with neural style transfer'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 33
year: '2025'
...
---
OA_type: closed access
_id: '19444'
abstract:
- lang: eng
  text: As the field of neural organoids and assembloids expands, there is an emergent
    need for guidance and advice on designing, conducting and reporting experiments
    to increase the reproducibility and utility of these models. In this Perspective,
    we present a framework for the experimental process that encompasses ensuring
    the quality and integrity of human pluripotent stem cells, characterizing and
    manipulating neural cells in vitro, transplantation techniques and considerations
    for modelling human development, evolution and disease. As with all scientific
    endeavours, we advocate for rigorous experimental designs tailored to explicit
    scientific questions as well as transparent methodologies and data sharing to
    provide useful knowledge for current research practices and for developing regulatory
    standards.
acknowledgement: The authors thank members of their laboratories who provided feedback
  on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L.
  Li, N. Caporale, E. Villa and M. Sutcliffe.
article_processing_charge: No
article_type: original
author:
- first_name: Sergiu P.
  full_name: Pașca, Sergiu P.
  last_name: Pașca
- first_name: Paola
  full_name: Arlotta, Paola
  last_name: Arlotta
- first_name: Helen S.
  full_name: Bateup, Helen S.
  last_name: Bateup
- first_name: J. Gray
  full_name: Camp, J. Gray
  last_name: Camp
- first_name: Silvia
  full_name: Cappello, Silvia
  last_name: Cappello
- first_name: Fred H.
  full_name: Gage, Fred H.
  last_name: Gage
- first_name: Jürgen A.
  full_name: Knoblich, Jürgen A.
  last_name: Knoblich
- first_name: Arnold R.
  full_name: Kriegstein, Arnold R.
  last_name: Kriegstein
- first_name: Madeline A.
  full_name: Lancaster, Madeline A.
  last_name: Lancaster
- first_name: Guo Li
  full_name: Ming, Guo Li
  last_name: Ming
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Hideyuki
  full_name: Okano, Hideyuki
  last_name: Okano
- first_name: Malin
  full_name: Parmar, Malin
  last_name: Parmar
- first_name: In Hyun
  full_name: Park, In Hyun
  last_name: Park
- first_name: Orly
  full_name: Reiner, Orly
  last_name: Reiner
- first_name: Hongjun
  full_name: Song, Hongjun
  last_name: Song
- first_name: Lorenz
  full_name: Studer, Lorenz
  last_name: Studer
- first_name: Jun
  full_name: Takahashi, Jun
  last_name: Takahashi
- first_name: Sally
  full_name: Temple, Sally
  last_name: Temple
- first_name: Giuseppe
  full_name: Testa, Giuseppe
  last_name: Testa
- first_name: Barbara
  full_name: Treutlein, Barbara
  last_name: Treutlein
- first_name: Flora M.
  full_name: Vaccarino, Flora M.
  last_name: Vaccarino
- first_name: Pierre
  full_name: Vanderhaeghen, Pierre
  last_name: Vanderhaeghen
- first_name: Tracy
  full_name: Young-Pearse, Tracy
  last_name: Young-Pearse
citation:
  ama: Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids
    and transplantation studies. <i>Nature</i>. 2025;639(8054):315-320. doi:<a href="https://doi.org/10.1038/s41586-024-08487-6">10.1038/s41586-024-08487-6</a>
  apa: Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage,
    F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids
    and transplantation studies. <i>Nature</i>. Springer Nature. <a href="https://doi.org/10.1038/s41586-024-08487-6">https://doi.org/10.1038/s41586-024-08487-6</a>
  chicago: Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia
    Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids,
    Assembloids and Transplantation Studies.” <i>Nature</i>. Springer Nature, 2025.
    <a href="https://doi.org/10.1038/s41586-024-08487-6">https://doi.org/10.1038/s41586-024-08487-6</a>.
  ieee: S. P. Pașca <i>et al.</i>, “A framework for neural organoids, assembloids
    and transplantation studies,” <i>Nature</i>, vol. 639, no. 8054. Springer Nature,
    pp. 315–320, 2025.
  ista: Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA,
    Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH,
    Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino
    FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids
    and transplantation studies. Nature. 639(8054), 315–320.
  mla: Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and
    Transplantation Studies.” <i>Nature</i>, vol. 639, no. 8054, Springer Nature,
    2025, pp. 315–20, doi:<a href="https://doi.org/10.1038/s41586-024-08487-6">10.1038/s41586-024-08487-6</a>.
  short: S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A.
    Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M.
    Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G.
    Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature
    639 (2025) 315–320.
date_created: 2025-03-23T23:01:27Z
date_published: 2025-03-13T00:00:00Z
date_updated: 2025-09-30T11:13:47Z
day: '13'
department:
- _id: GaNo
doi: 10.1038/s41586-024-08487-6
external_id:
  isi:
  - '001437461900001'
  pmid:
  - '39653126'
intvolume: '       639'
isi: 1
issue: '8054'
language:
- iso: eng
month: '03'
oa_version: None
page: 315-320
pmid: 1
publication: Nature
publication_identifier:
  eissn:
  - 1476-4687
  issn:
  - 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A framework for neural organoids, assembloids and transplantation studies
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 639
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19445'
abstract:
- lang: eng
  text: "In reconfiguration, we are given two solutions to a graph problem, such as
    Vertex Cover or Dominating Set, with each solution represented by a placement
    of tokens on vertices of the graph. Our task is to reconfigure one into the other
    using small steps while ensuring the intermediate configurations of tokens are
    also valid solutions. The two commonly studied settings are Token Jumping and
    Token Sliding, which allows moving a single token to an arbitrary or an adjacent
    vertex, respectively.\r\n\r\nWe introduce new rules that generalize Token Jumping,
    parameterized by the number of tokens allowed to move at once and by the maximum
    distance of each move. Our main contribution is identifying minimal rules that
    allow reconfiguring any possible given solution into any other for Independent
    Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide
    an efficient algorithm that finds a corresponding reconfiguration sequence.\r\n\r\nWe
    further focus on the rule that allows each token to move to an adjacent vertex
    in a single step. This natural variant turns out to be the minimal rule that guarantees
    reconfigurability for Vertex Cover. We determine the computational complexity
    of deciding whether a (shortest) reconfiguration sequence exists under this rule
    for the three studied problems. While reachability for Vertex Cover is shown to
    be in P, finding a shortest sequence is shown to be NP-complete. For Independent
    Set and Dominating Set, even reachability is shown to be PSPACE-complete."
acknowledgement: J. M. Křišťan acknowledges the support of the Czech Science Foundation
  Grant No. 24-12046S. This work was supported by the Grant Agency of the Czech Technical
  University in Prague, grant No. SGS23/205/OHK3/3T/18. J. Svoboda acknowledges the
  support of the ERC CoG 863818 (ForM-SMArt) grant.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Jan Matyáš
  full_name: Křišťan, Jan Matyáš
  last_name: Křišťan
- first_name: Jakub
  full_name: Svoboda, Jakub
  id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
  last_name: Svoboda
  orcid: 0000-0002-1419-3267
citation:
  ama: 'Křišťan JM, Svoboda J. Reconfiguration using generalized token jumping. In:
    <i>19th International Conference and Workshops on Algorithms and Computation</i>.
    Vol 15411. Springer Nature; 2025:244-265. doi:<a href="https://doi.org/10.1007/978-981-96-2845-2_16">10.1007/978-981-96-2845-2_16</a>'
  apa: 'Křišťan, J. M., &#38; Svoboda, J. (2025). Reconfiguration using generalized
    token jumping. In <i>19th International Conference and Workshops on Algorithms
    and Computation</i> (Vol. 15411, pp. 244–265). Chengdu, China: Springer Nature.
    <a href="https://doi.org/10.1007/978-981-96-2845-2_16">https://doi.org/10.1007/978-981-96-2845-2_16</a>'
  chicago: Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized
    Token Jumping.” In <i>19th International Conference and Workshops on Algorithms
    and Computation</i>, 15411:244–65. Springer Nature, 2025. <a href="https://doi.org/10.1007/978-981-96-2845-2_16">https://doi.org/10.1007/978-981-96-2845-2_16</a>.
  ieee: J. M. Křišťan and J. Svoboda, “Reconfiguration using generalized token jumping,”
    in <i>19th International Conference and Workshops on Algorithms and Computation</i>,
    Chengdu, China, 2025, vol. 15411, pp. 244–265.
  ista: 'Křišťan JM, Svoboda J. 2025. Reconfiguration using generalized token jumping.
    19th International Conference and Workshops on Algorithms and Computation. WALCOM:
    International Conference and Workshops on Algorithms and Computation, LNCS, vol.
    15411, 244–265.'
  mla: Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized
    Token Jumping.” <i>19th International Conference and Workshops on Algorithms and
    Computation</i>, vol. 15411, Springer Nature, 2025, pp. 244–65, doi:<a href="https://doi.org/10.1007/978-981-96-2845-2_16">10.1007/978-981-96-2845-2_16</a>.
  short: J.M. Křišťan, J. Svoboda, in:, 19th International Conference and Workshops
    on Algorithms and Computation, Springer Nature, 2025, pp. 244–265.
conference:
  end_date: 2025-03-02
  location: Chengdu, China
  name: 'WALCOM: International Conference and Workshops on Algorithms and Computation'
  start_date: 2025-02-28
date_created: 2025-03-23T23:01:27Z
date_published: 2025-02-20T00:00:00Z
date_updated: 2025-09-30T11:14:33Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-981-96-2845-2_16
ec_funded: 1
external_id:
  arxiv:
  - '2411.12582'
  isi:
  - '001537885900016'
intvolume: '     15411'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2411.12582
month: '02'
oa: 1
oa_version: Preprint
page: 244-265
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '863818'
  name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 19th International Conference and Workshops on Algorithms and Computation
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9789819628445'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconfiguration using generalized token jumping
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15411
year: '2025'
...
---
APC_amount: 3317,75 EUR
OA_place: publisher
OA_type: hybrid
_id: '19453'
abstract:
- lang: eng
  text: A key feature of biological and artificial neural networks is the progressive
    refinement of their neural representations with experience. In neuroscience, this
    fact has inspired several recent studies in sensory and motor systems. However,
    less is known about how higher associational cortical areas, such as the hippocampus,
    modify representations throughout the learning of complex tasks. Here, we focus
    on associative learning, a process that requires forming a connection between
    the representations of different variables for appropriate behavioral response.
    We trained rats in a space-context associative task and monitored hippocampal
    neural activity throughout the entire learning period, over several days. This
    allowed us to assess changes in the representations of context, movement direction,
    and position, as well as their relationship to behavior. We identified a hierarchical
    representational structure in the encoding of these three task variables that
    was preserved throughout learning. Nevertheless, we also observed changes at the
    lower levels of the hierarchy where context was encoded. These changes were local
    in neural activity space and restricted to physical positions where context identification
    was necessary for correct decision-making, supporting better context decoding
    and contextual code compression. Our results demonstrate that the hippocampal
    code not only accommodates hierarchical relationships between different variables
    but also enables efficient learning through minimal changes in neural activity
    space. Beyond the hippocampus, our work reveals a representation learning mechanism
    that might be implemented in other biological and artificial networks performing
    similar tasks.
acknowledgement: We would like to thank Rebecca Morse for performing the recordings
  in one of the animals under the supervision of H.S.C.C., Jago Wallenschus for the
  technical support, especially with maze design, Wiktor Mlynarski for the advice
  and discussions and Andrea Cumpelik for suggestions during the writing. M.N. was
  supported by the Howard Hughes Medical Institute. H.S.C.C. received funding from
  the European Union’s Horizon 2020 research and innovation programme under the Marie
  Skłodowska-Curie grant agreement No 665385.
article_number: e2417025122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Heloisa
  full_name: Chiossi, Heloisa
  id: 2BBA502C-F248-11E8-B48F-1D18A9856A87
  last_name: Chiossi
  orcid: 0009-0004-2973-278X
- first_name: Michele
  full_name: Nardin, Michele
  id: 30BD0376-F248-11E8-B48F-1D18A9856A87
  last_name: Nardin
  orcid: 0000-0001-8849-6570
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Jozsef L
  full_name: Csicsvari, Jozsef L
  id: 3FA14672-F248-11E8-B48F-1D18A9856A87
  last_name: Csicsvari
  orcid: 0000-0002-5193-4036
citation:
  ama: Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal
    representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>.
    2025;122(11). doi:<a href="https://doi.org/10.1073/pnas.2417025122">10.1073/pnas.2417025122</a>
  apa: Chiossi, H. S. C., Nardin, M., Tkačik, G., &#38; Csicsvari, J. L. (2025). Learning
    reshapes the hippocampal representation hierarchy. <i>Proceedings of the National
    Academy of Sciences</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.2417025122">https://doi.org/10.1073/pnas.2417025122</a>
  chicago: Chiossi, Heloisa S. C., Michele Nardin, Gašper Tkačik, and Jozsef L Csicsvari.
    “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of
    the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href="https://doi.org/10.1073/pnas.2417025122">https://doi.org/10.1073/pnas.2417025122</a>.
  ieee: H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes
    the hippocampal representation hierarchy,” <i>Proceedings of the National Academy
    of Sciences</i>, vol. 122, no. 11. National Academy of Sciences, 2025.
  ista: Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. 2025. Learning reshapes the
    hippocampal representation hierarchy. Proceedings of the National Academy of Sciences.
    122(11), e2417025122.
  mla: Chiossi, Heloisa S. C., et al. “Learning Reshapes the Hippocampal Representation
    Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122,
    no. 11, e2417025122, National Academy of Sciences, 2025, doi:<a href="https://doi.org/10.1073/pnas.2417025122">10.1073/pnas.2417025122</a>.
  short: H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the
    National Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-03-25T07:38:35Z
date_published: 2025-03-10T00:00:00Z
date_updated: 2026-05-06T13:12:01Z
day: '10'
ddc:
- '570'
department:
- _id: GaTk
- _id: JoCs
doi: 10.1073/pnas.2417025122
ec_funded: 1
external_id:
  isi:
  - '001459499500001'
  pmid:
  - '40063792'
file:
- access_level: open_access
  checksum: 1217207c254553154faa065964990988
  content_type: application/pdf
  creator: dernst
  date_created: 2025-03-25T07:49:04Z
  date_updated: 2025-03-25T07:49:04Z
  file_id: '19454'
  file_name: 2025_PNAS_Chiossi.pdf
  file_size: 1553502
  relation: main_file
  success: 1
file_date_updated: 2025-03-25T07:49:04Z
has_accepted_license: '1'
intvolume: '       122'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/hchiossi/hpc-hierarchy
  record:
  - id: '18991'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Learning reshapes the hippocampal representation hierarchy
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: 122
year: '2025'
...
---
OA_type: closed access
_id: '19465'
article_number: '415'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carrie A
  full_name: Bernecky, Carrie A
  id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
  last_name: Bernecky
  orcid: 0000-0003-0893-7036
citation:
  ama: Bernecky C. Understanding the machinery that reads the genome. <i>Nature Reviews
    Molecular Cell Biology</i>. 2025;26. doi:<a href="https://doi.org/10.1038/s41580-025-00844-1">10.1038/s41580-025-00844-1</a>
  apa: Bernecky, C. (2025). Understanding the machinery that reads the genome. <i>Nature
    Reviews Molecular Cell Biology</i>. Springer Nature. <a href="https://doi.org/10.1038/s41580-025-00844-1">https://doi.org/10.1038/s41580-025-00844-1</a>
  chicago: Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.”
    <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2025. <a href="https://doi.org/10.1038/s41580-025-00844-1">https://doi.org/10.1038/s41580-025-00844-1</a>.
  ieee: C. Bernecky, “Understanding the machinery that reads the genome,” <i>Nature
    Reviews Molecular Cell Biology</i>, vol. 26. Springer Nature, 2025.
  ista: Bernecky C. 2025. Understanding the machinery that reads the genome. Nature
    Reviews Molecular Cell Biology. 26, 415.
  mla: Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” <i>Nature
    Reviews Molecular Cell Biology</i>, vol. 26, 415, Springer Nature, 2025, doi:<a
    href="https://doi.org/10.1038/s41580-025-00844-1">10.1038/s41580-025-00844-1</a>.
  short: C. Bernecky, Nature Reviews Molecular Cell Biology 26 (2025).
corr_author: '1'
date_created: 2025-03-31T10:07:22Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2025-09-30T11:20:36Z
day: '01'
department:
- _id: CaBe
doi: 10.1038/s41580-025-00844-1
external_id:
  isi:
  - '001455740100001'
  pmid:
  - '40155512'
intvolume: '        26'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
  eissn:
  - 1471-0080
  issn:
  - 1471-0072
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Understanding the machinery that reads the genome
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2025'
...
---
OA_place: publisher
_id: '19478'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "This project was funded by the European Research Council Advanced
  Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian
  Science Fund (FWF; P\r\n37051-B)."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Huihuang
  full_name: Chen, Huihuang
  id: 83c96512-15b2-11ec-abd3-b7eede36184f
  last_name: Chen
citation:
  ama: Chen H. The cAMP second messenger in auxin signalling. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19478">10.15479/AT-ISTA-19478</a>
  apa: Chen, H. (2025). <i>The cAMP second messenger in auxin signalling</i>. Institute
    of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-19478">https://doi.org/10.15479/AT-ISTA-19478</a>
  chicago: Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute
    of Science and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT-ISTA-19478">https://doi.org/10.15479/AT-ISTA-19478</a>.
  ieee: H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science
    and Technology Austria, 2025.
  ista: Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of
    Science and Technology Austria.
  mla: Chen, Huihuang. <i>The CAMP Second Messenger in Auxin Signalling</i>. Institute
    of Science and Technology Austria, 2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-19478">10.15479/AT-ISTA-19478</a>.
  short: H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science
    and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-04-04T07:48:24Z
date_published: 2025-04-04T00:00:00Z
date_updated: 2026-04-28T13:42:45Z
day: '04'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/AT-ISTA-19478
ec_funded: 1
file:
- access_level: closed
  checksum: b154973663a1bba505683faab7ae5ead
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: hchen
  date_created: 2025-04-08T08:00:07Z
  date_updated: 2025-04-08T08:22:37Z
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has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa_version: Published Version
page: '118'
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
  grant_number: '101142681'
  name: Cyclic nucleotides as second messengers in plants
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '13212'
    relation: part_of_dissertation
    status: public
  - id: '19421'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
title: The cAMP second messenger in auxin signalling
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19483'
abstract:
- lang: eng
  text: We prove matching upper and lower bounds for the average of the6-torsionof
    class groups of quadratic fields. Furthermore, we count the number of integer
    solutions on an affine quartic threefold.
article_number: '18'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yik Tung
  full_name: Chan, Yik Tung
  id: c4c0afc8-9262-11ed-9231-d8b0bc743af1
  last_name: Chan
  orcid: 0000-0001-8467-4106
- first_name: Peter
  full_name: Koymans, Peter
  last_name: Koymans
- first_name: Carlo
  full_name: Pagano, Carlo
  last_name: Pagano
- first_name: Efthymios
  full_name: Sofos, Efthymios
  last_name: Sofos
citation:
  ama: Chan S, Koymans P, Pagano C, Sofos E. 6-torision and integral points on quartic
    threefolds. <i>Annali della Scuola Normale Superiore di Pisa, Classe di Scienze</i>.
    2025. doi:<a href="https://doi.org/10.2422/2036-2145.202412_006">10.2422/2036-2145.202412_006</a>
  apa: Chan, S., Koymans, P., Pagano, C., &#38; Sofos, E. (2025). 6-torision and integral
    points on quartic threefolds. <i>Annali Della Scuola Normale Superiore Di Pisa,
    Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale. <a href="https://doi.org/10.2422/2036-2145.202412_006">https://doi.org/10.2422/2036-2145.202412_006</a>
  chicago: Chan, Stephanie, Peter Koymans, Carlo Pagano, and Efthymios Sofos. “6-Torision
    and Integral Points on Quartic Threefolds.” <i>Annali Della Scuola Normale Superiore
    Di Pisa, Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale,
    2025. <a href="https://doi.org/10.2422/2036-2145.202412_006">https://doi.org/10.2422/2036-2145.202412_006</a>.
  ieee: S. Chan, P. Koymans, C. Pagano, and E. Sofos, “6-torision and integral points
    on quartic threefolds,” <i>Annali della Scuola Normale Superiore di Pisa, Classe
    di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale, 2025.
  ista: Chan S, Koymans P, Pagano C, Sofos E. 2025. 6-torision and integral points
    on quartic threefolds. Annali della Scuola Normale Superiore di Pisa, Classe di
    Scienze., 18.
  mla: Chan, Stephanie, et al. “6-Torision and Integral Points on Quartic Threefolds.”
    <i>Annali Della Scuola Normale Superiore Di Pisa, Classe Di Scienze</i>, 18, Scuola
    Normale Superiore - Edizioni della Normale, 2025, doi:<a href="https://doi.org/10.2422/2036-2145.202412_006">10.2422/2036-2145.202412_006</a>.
  short: S. Chan, P. Koymans, C. Pagano, E. Sofos, Annali Della Scuola Normale Superiore
    Di Pisa, Classe Di Scienze (2025).
corr_author: '1'
date_created: 2025-04-05T10:49:27Z
date_published: 2025-03-07T00:00:00Z
date_updated: 2025-05-14T11:40:24Z
day: '07'
department:
- _id: TiBr
doi: 10.2422/2036-2145.202412_006
external_id:
  arxiv:
  - '2403.13359'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.2403.13359'
month: '03'
oa: 1
oa_version: Preprint
publication: Annali della Scuola Normale Superiore di Pisa, Classe di Scienze
publication_identifier:
  eissn:
  - 2036-2145
  issn:
  - 0391-173X
publication_status: epub_ahead
publisher: Scuola Normale Superiore - Edizioni della Normale
status: public
title: 6-torision and integral points on quartic threefolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19495'
abstract:
- lang: eng
  text: Machine learning interatomic potentials (MLIPs) often neglect long-range interactions,
    such as electrostatic and dispersion forces. In this work, we introduce a straightforward
    and efficient method to account for long-range interactions by learning a hidden
    variable from local atomic descriptors and applying an Ewald summation to this
    variable. We demonstrate that in systems including charged and polar molecular
    dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can
    lead to unphysical predictions even when employing message passing. The long-range
    models effectively eliminate these artifacts, with only about twice the computational
    cost of short-range MLIPs.
acknowledgement: B. C. thanks David Limmer for providing the water slab dataset, and
  Carolin Faller for the NaCl dataset.
article_number: '80'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
citation:
  ama: Cheng B. Latent Ewald summation for machine learning of long-range interactions.
    <i>npj Computational Materials</i>. 2025;11. doi:<a href="https://doi.org/10.1038/s41524-025-01577-7">10.1038/s41524-025-01577-7</a>
  apa: Cheng, B. (2025). Latent Ewald summation for machine learning of long-range
    interactions. <i>Npj Computational Materials</i>. Springer Nature. <a href="https://doi.org/10.1038/s41524-025-01577-7">https://doi.org/10.1038/s41524-025-01577-7</a>
  chicago: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range
    Interactions.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href="https://doi.org/10.1038/s41524-025-01577-7">https://doi.org/10.1038/s41524-025-01577-7</a>.
  ieee: B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,”
    <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025.
  ista: Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions.
    npj Computational Materials. 11, 80.
  mla: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range
    Interactions.” <i>Npj Computational Materials</i>, vol. 11, 80, Springer Nature,
    2025, doi:<a href="https://doi.org/10.1038/s41524-025-01577-7">10.1038/s41524-025-01577-7</a>.
  short: B. Cheng, Npj Computational Materials 11 (2025).
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-03-26T00:00:00Z
date_updated: 2025-09-30T11:31:47Z
day: '26'
ddc:
- '000'
department:
- _id: BiCh
doi: 10.1038/s41524-025-01577-7
external_id:
  arxiv:
  - '2408.15165'
  isi:
  - '001453622900002'
file:
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  checksum: cc99b7407a12139d9b2d8457961935ae
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  creator: dernst
  date_created: 2025-04-08T09:34:58Z
  date_updated: 2025-04-08T09:34:58Z
  file_id: '19528'
  file_name: 2025_npjCompMaterials_Cheng.pdf
  file_size: 1608315
  relation: main_file
  success: 1
file_date_updated: 2025-04-08T09:34:58Z
has_accepted_license: '1'
intvolume: '        11'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: npj Computational Materials
publication_identifier:
  eissn:
  - 2057-3960
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Latent Ewald summation for machine learning of long-range interactions
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19496'
abstract:
- lang: eng
  text: We introduce the notions of scale for sets and measures on metric space by
    generalizing the usual notions of dimension. Several versions of scales are introduced
    such as Hausdorff, packing, box, local and quantization. They are defined for
    different growth, allowing a refined study of infinite dimensional spaces. We
    prove general theorems comparing the different versions of scales. They are applied
    to describe geometries of ergodic decompositions, of the Wiener measure and from
    functional spaces. The first application solves a problem of Berger on the notions
    of emergence (2020); the second lies in the geometry of the Wiener measure and
    extends the work of Dereich–Lifshits (2005); the last refines Kolmogorov–Tikhomirov
    (1958) study on finitely differentiable functions.
article_number: '15'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Mathieu
  full_name: Helfter, Mathieu
  id: 7d296fbe-e2c6-11ee-84d3-d5c2945f9a57
  last_name: Helfter
citation:
  ama: Helfter M. Scales. <i>Mathematische Zeitschrift</i>. 2025;310. doi:<a href="https://doi.org/10.1007/s00209-025-03719-5">10.1007/s00209-025-03719-5</a>
  apa: Helfter, M. (2025). Scales. <i>Mathematische Zeitschrift</i>. Springer Nature.
    <a href="https://doi.org/10.1007/s00209-025-03719-5">https://doi.org/10.1007/s00209-025-03719-5</a>
  chicago: Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>. Springer
    Nature, 2025. <a href="https://doi.org/10.1007/s00209-025-03719-5">https://doi.org/10.1007/s00209-025-03719-5</a>.
  ieee: M. Helfter, “Scales,” <i>Mathematische Zeitschrift</i>, vol. 310. Springer
    Nature, 2025.
  ista: Helfter M. 2025. Scales. Mathematische Zeitschrift. 310, 15.
  mla: Helfter, Mathieu. “Scales.” <i>Mathematische Zeitschrift</i>, vol. 310, 15,
    Springer Nature, 2025, doi:<a href="https://doi.org/10.1007/s00209-025-03719-5">10.1007/s00209-025-03719-5</a>.
  short: M. Helfter, Mathematische Zeitschrift 310 (2025).
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-09-30T11:31:00Z
day: '01'
department:
- _id: VaKa
doi: 10.1007/s00209-025-03719-5
external_id:
  arxiv:
  - '2206.05231'
  isi:
  - '001450830300001'
intvolume: '       310'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2206.05231
month: '05'
oa: 1
oa_version: Preprint
publication: Mathematische Zeitschrift
publication_identifier:
  eissn:
  - 1432-1823
  issn:
  - 0025-5874
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scales
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 310
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19497'
abstract:
- lang: eng
  text: The stochastic gravitational wave (GW) background recently discovered by several
    pulsar timing array experiments is consistent with arising from a population of
    coalescing super-massive black hole binaries. The amplitude of the background
    is somewhat higher than expected in most previous population models or from the
    local mass density observations. Such binaries are expected to be produced in
    galaxy mergers, which are also thought to trigger bright quasar activity. Under
    the assumptions that (i) a fraction fbin∼1 of all quasars are associated with
    mergers, (ii) the typical quasar lifetime is tQ∼108 yr, and (iii) adopting Eddington
    ratios fEdd∼0.25 for the luminosity of quasars, we compute the GW background associated
    directly with the empirically measured quasar luminosity function. This approach
    bypasses the need to model the cosmological evolution of black holes or galaxy
    mergers from simulations or semi-analytical models. We find the amplitude matching
    the value measured by NANOGrav. Our results are consistent with most quasars being
    associated with black hole binaries and being the sources of the GW background,
    and imply a joint constraint on tQ, fEdd and the typical mass ratio q≡M2/M1. The
    signal in this case would be dominated by relatively distant ∼109M⊙ sources at
    z≈2−3, at the peak of quasar activity. Similarly to other models, our results
    remain in tension with the local super-massive black hole mass density.
acknowledgement: We thank Chengcheng Xin and Girish Kulkarni for useful discussions.
  ZH gratefully acknowledges the hospitality of Eötvös University during an extended
  sabbatical visit, where this work began. ZH acknowledges support from NSF Grant
  AST-2006176 and NASA Grants 80NSSC22K0822 and 80NSSC24K0440. ZF acknowledges support
  from the Hungarian National Research, Development and Innovation Office (NKFIH)
  through the Institutional Excellence Program No. TKP2021-NKTA-64.
article_number: '075007'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ágnes
  full_name: Kis-Tóth, Ágnes
  last_name: Kis-Tóth
- first_name: Zoltán
  full_name: Haiman, Zoltán
  id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
  last_name: Haiman
  orcid: 0000-0003-3633-5403
- first_name: Zsolt
  full_name: Frei, Zsolt
  last_name: Frei
citation:
  ama: Kis-Tóth Á, Haiman Z, Frei Z. Can quasars, triggered by mergers, account for
    NANOGrav’s stochastic gravitational wave background? <i>Classical and Quantum
    Gravity</i>. 2025;42(7). doi:<a href="https://doi.org/10.1088/1361-6382/adbda6">10.1088/1361-6382/adbda6</a>
  apa: Kis-Tóth, Á., Haiman, Z., &#38; Frei, Z. (2025). Can quasars, triggered by
    mergers, account for NANOGrav’s stochastic gravitational wave background? <i>Classical
    and Quantum Gravity</i>. IOP Publishing. <a href="https://doi.org/10.1088/1361-6382/adbda6">https://doi.org/10.1088/1361-6382/adbda6</a>
  chicago: Kis-Tóth, Ágnes, Zoltán Haiman, and Zsolt Frei. “Can Quasars, Triggered
    by Mergers, Account for NANOGrav’s Stochastic Gravitational Wave Background?”
    <i>Classical and Quantum Gravity</i>. IOP Publishing, 2025. <a href="https://doi.org/10.1088/1361-6382/adbda6">https://doi.org/10.1088/1361-6382/adbda6</a>.
  ieee: Á. Kis-Tóth, Z. Haiman, and Z. Frei, “Can quasars, triggered by mergers, account
    for NANOGrav’s stochastic gravitational wave background?,” <i>Classical and Quantum
    Gravity</i>, vol. 42, no. 7. IOP Publishing, 2025.
  ista: Kis-Tóth Á, Haiman Z, Frei Z. 2025. Can quasars, triggered by mergers, account
    for NANOGrav’s stochastic gravitational wave background? Classical and Quantum
    Gravity. 42(7), 075007.
  mla: Kis-Tóth, Ágnes, et al. “Can Quasars, Triggered by Mergers, Account for NANOGrav’s
    Stochastic Gravitational Wave Background?” <i>Classical and Quantum Gravity</i>,
    vol. 42, no. 7, 075007, IOP Publishing, 2025, doi:<a href="https://doi.org/10.1088/1361-6382/adbda6">10.1088/1361-6382/adbda6</a>.
  short: Á. Kis-Tóth, Z. Haiman, Z. Frei, Classical and Quantum Gravity 42 (2025).
date_created: 2025-04-06T22:01:32Z
date_published: 2025-04-04T00:00:00Z
date_updated: 2025-09-30T11:30:11Z
day: '04'
department:
- _id: ZoHa
doi: 10.1088/1361-6382/adbda6
external_id:
  arxiv:
  - '2412.12726'
  isi:
  - '001448904700001'
intvolume: '        42'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2412.12726
month: '04'
oa: 1
oa_version: Preprint
publication: Classical and Quantum Gravity
publication_identifier:
  eissn:
  - 1361-6382
  issn:
  - 0264-9381
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can quasars, triggered by mergers, account for NANOGrav’s stochastic gravitational
  wave background?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19499'
abstract:
- lang: eng
  text: Quantum hardware is inherently fragile and noisy. We find that the accuracy
    of traditional quantum error correction algorithms can be improved depending on
    the hardware. Given different hardware specifications, we automatically synthesize
    hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger)
    state preparation. Using stochastic techniques from computer science, our method
    presents a computational tool to compute exact accuracy guarantees and synthesize
    optimal algorithms that are often different from traditional ones. We also show
    that improvements can be gained with respect to the Qiskit transpiler as we compute
    the hardware-optimal qubit mapping for the GHZ state-preparation problem.
acknowledgement: We thank the reviewers. In particular, they inspired us to analyze
  the reset and state-preparation problems, to compute optimal qubit mappings, and
  to apply our method to a quantum error correction scheme that includes both bitflip
  and phaseflip corrections. We also thank Raimundo Saona and Marek Chalupa for their
  time spent in insightful discussions. This research was partially supported by the
  European Research Council CoG 863818 (ForM-SMArt) grant.
article_number: e2419273122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Stefanie
  full_name: Muroya Lei, Stefanie
  id: a376de31-8972-11ed-ae7b-d0251c13c8ff
  last_name: Muroya Lei
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
citation:
  ama: Muroya Lei S, Chatterjee K, Henzinger TA. Hardware-optimal quantum algorithms.
    <i>Proceedings of the National Academy of Sciences</i>. 2025;122(12). doi:<a href="https://doi.org/10.1073/pnas.2419273122">10.1073/pnas.2419273122</a>
  apa: Muroya Lei, S., Chatterjee, K., &#38; Henzinger, T. A. (2025). Hardware-optimal
    quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. National
    Academy of Sciences. <a href="https://doi.org/10.1073/pnas.2419273122">https://doi.org/10.1073/pnas.2419273122</a>
  chicago: Muroya Lei, Stefanie, Krishnendu Chatterjee, and Thomas A Henzinger. “Hardware-Optimal
    Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>. National
    Academy of Sciences, 2025. <a href="https://doi.org/10.1073/pnas.2419273122">https://doi.org/10.1073/pnas.2419273122</a>.
  ieee: S. Muroya Lei, K. Chatterjee, and T. A. Henzinger, “Hardware-optimal quantum
    algorithms,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122,
    no. 12. National Academy of Sciences, 2025.
  ista: Muroya Lei S, Chatterjee K, Henzinger TA. 2025. Hardware-optimal quantum algorithms.
    Proceedings of the National Academy of Sciences. 122(12), e2419273122.
  mla: Muroya Lei, Stefanie, et al. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings
    of the National Academy of Sciences</i>, vol. 122, no. 12, e2419273122, National
    Academy of Sciences, 2025, doi:<a href="https://doi.org/10.1073/pnas.2419273122">10.1073/pnas.2419273122</a>.
  short: S. Muroya Lei, K. Chatterjee, T.A. Henzinger, Proceedings of the National
    Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-04-06T22:01:32Z
date_published: 2025-03-25T00:00:00Z
date_updated: 2026-04-28T13:41:14Z
day: '25'
ddc:
- '000'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1073/pnas.2419273122
ec_funded: 1
external_id:
  isi:
  - '001459435600001'
  pmid:
  - '40106357'
file:
- access_level: open_access
  checksum: 83501b8a65ee5fdd3f5604fc28eddc22
  content_type: application/pdf
  creator: dernst
  date_created: 2025-04-07T11:42:22Z
  date_updated: 2025-04-07T11:42:22Z
  file_id: '19524'
  file_name: 2025_PNAS_Muroya.pdf
  file_size: 6805668
  relation: main_file
  success: 1
file_date_updated: 2025-04-07T11:42:22Z
has_accepted_license: '1'
intvolume: '       122'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
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: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/smml1996/algorithm_synthesis
  - description: News on ISTA website
    relation: press_release
    url: https://ista.ac.at/en/news/hardware-optimal-quantum-algorithms/
scopus_import: '1'
status: public
title: Hardware-optimal quantum algorithms
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 122
year: '2025'
...