---
OA_embargo: 6 months
OA_place: publisher
OA_type: hybrid
_id: '18305'
abstract:
- lang: eng
  text: Motor circuits represent the main output of the central nervous system and
    produce dynamic behaviors ranging from relatively simple rhythmic activities like
    swimming in fish and breathing in mammals to highly sophisticated dexterous movements
    in humans. Despite decades of research, the development and function of motor
    circuits remain poorly understood. Breakthroughs in the field recently provided
    new tools and tractable model systems that set the stage to discover the molecular
    mechanisms and circuit logic underlying motor control. Here, we describe recent
    advances from both vertebrate (mouse, frog) and invertebrate (nematode, fruit
    fly) systems on cellular and molecular mechanisms that enable motor circuits to
    develop and function and highlight conserved and divergent mechanisms necessary
    for motor circuit development.
acknowledgement: Work in the authors’ labs is funded by the Helmholtz Association
  (N.Z.), National Institute of Neurological Disorders and Stroke (NINDS) R01NS116365
  (P.K.), NINDS R01NS123439 and National Science Foundation IOS-2048080 (R.C.), NINDS
  R01NS114510 (P.P.), Natural Sciences and Engineering Research Council of Canada
  RGPIN-2021-03154 (K.M.) and Horizon Europe European Research Council Starting Grant
  Number 101041551 (L.B.S.). P.P. is the Weidenthal Family Designated Professor in
  Career Development.
article_number: e1238242024
article_processing_charge: No
article_type: original
author:
- first_name: Paschalis
  full_name: Kratsios, Paschalis
  last_name: Kratsios
- first_name: Niccolò
  full_name: Zampieri, Niccolò
  last_name: Zampieri
- first_name: Robert
  full_name: Carrillo, Robert
  last_name: Carrillo
- first_name: Kota
  full_name: Mizumoto, Kota
  last_name: Mizumoto
- first_name: Lora Beatrice Jaeger
  full_name: Sweeney, Lora Beatrice Jaeger
  id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
  last_name: Sweeney
  orcid: 0000-0001-9242-5601
- first_name: Polyxeni
  full_name: Philippidou, Polyxeni
  last_name: Philippidou
citation:
  ama: Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P.
    Molecular and cellular mechanisms of motor circuit development. <i>The Journal
    of Neuroscience</i>. 2024;44(40). doi:<a href="https://doi.org/10.1523/JNEUROSCI.1238-24.2024">10.1523/JNEUROSCI.1238-24.2024</a>
  apa: Kratsios, P., Zampieri, N., Carrillo, R., Mizumoto, K., Sweeney, L. B., &#38;
    Philippidou, P. (2024). Molecular and cellular mechanisms of motor circuit development.
    <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href="https://doi.org/10.1523/JNEUROSCI.1238-24.2024">https://doi.org/10.1523/JNEUROSCI.1238-24.2024</a>
  chicago: Kratsios, Paschalis, Niccolò Zampieri, Robert Carrillo, Kota Mizumoto,
    Lora B. Sweeney, and Polyxeni Philippidou. “Molecular and Cellular Mechanisms
    of Motor Circuit Development.” <i>The Journal of Neuroscience</i>. Society for
    Neuroscience, 2024. <a href="https://doi.org/10.1523/JNEUROSCI.1238-24.2024">https://doi.org/10.1523/JNEUROSCI.1238-24.2024</a>.
  ieee: P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L. B. Sweeney, and P.
    Philippidou, “Molecular and cellular mechanisms of motor circuit development,”
    <i>The Journal of Neuroscience</i>, vol. 44, no. 40. Society for Neuroscience,
    2024.
  ista: Kratsios P, Zampieri N, Carrillo R, Mizumoto K, Sweeney LB, Philippidou P.
    2024. Molecular and cellular mechanisms of motor circuit development. The Journal
    of Neuroscience. 44(40), e1238242024.
  mla: Kratsios, Paschalis, et al. “Molecular and Cellular Mechanisms of Motor Circuit
    Development.” <i>The Journal of Neuroscience</i>, vol. 44, no. 40, e1238242024,
    Society for Neuroscience, 2024, doi:<a href="https://doi.org/10.1523/JNEUROSCI.1238-24.2024">10.1523/JNEUROSCI.1238-24.2024</a>.
  short: P. Kratsios, N. Zampieri, R. Carrillo, K. Mizumoto, L.B. Sweeney, P. Philippidou,
    The Journal of Neuroscience 44 (2024).
date_created: 2024-10-13T22:01:49Z
date_published: 2024-10-02T00:00:00Z
date_updated: 2026-01-05T14:01:26Z
day: '02'
ddc:
- '570'
department:
- _id: LoSw
doi: 10.1523/JNEUROSCI.1238-24.2024
external_id:
  isi:
  - '001335212200016'
  pmid:
  - '39358025'
has_accepted_license: '1'
intvolume: '        44'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1523/JNEUROSCI.1238-24.2024
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
  grant_number: '101041551'
  name: Development and Evolution of Tetrapod Motor Circuits
publication: The Journal of Neuroscience
publication_identifier:
  eissn:
  - 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and cellular mechanisms of motor circuit development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18306'
abstract:
- lang: eng
  text: Neutral sodium (Na i) is an alkali metal with a favorable absorption cross
    section such that tenuous gases are easily illuminated at select transiting exoplanet
    systems. We examine both the time-averaged and time-series alkali spectral flux
    individually, over 4 nights at a hot Saturn system on a ∼2.8 day orbit about a
    Sun-like star WASP-49 A. Very Large Telescope/ESPRESSO observations are analyzed,
    providing new constraints. We recover the previously confirmed residual sodium
    flux uniquely when averaged, whereas night-to-night Na i varies by more than an
    order of magnitude. On HARPS/3.6 m Epoch II, we report a Doppler redshift at vΓ,NaD
    = + 9.7 ± 1.6 km s−1 with respect to the planet's rest frame. Upon examining the
    lightcurves, we confirm night-to-night variability, on the order of ∼1%–4% in
    NaD, rarely coinciding with exoplanet transit, not readily explained by stellar
    activity, starspots, tellurics, or the interstellar medium. Coincident with the
    ∼+10 km s−1 Doppler redshift, we detect a transient sodium absorption event dFNaD/F⋆
    = 3.6% ± 1% at a relative difference of ΔFNaD(t) ∼ 4.4% ± 1%, lasting ΔtNaD ≳
    40 minutes. Since exoplanetary alkali signatures are blueshifted due to the natural
    vector of radiation pressure, estimated here at roughly ∼−5.7 km s−1, the radial
    velocity is rather at +15.4 km s−1, far larger than any known exoplanet system.
    Given that the redshift magnitude vΓ is in between the Roche limit and dynamically
    stable satellite orbits, the transient sodium may be a putative indication of
    a natural satellite orbiting WASP-49 A b.
acknowledgement: The research described in this Letter was carried out in part at
  the Jet Propulsion Laboratory, California Institute of Technology, under a contract
  with the National Aeronautics Space Administration, © 2024. California Institute
  of Technology. Government sponsorship acknowledged. A.V.O. and J.V.S. thank M. Lendl
  for constraints and discussions on the mass of WASP-49 A b. S.G.S acknowledges the
  support from FCT through Investigador FCT contract nr. CEECIND/00826/2018 and POPH/FSE
  (EC).
article_number: L53
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Apurva V.
  full_name: Oza, Apurva V.
  last_name: Oza
- first_name: Julia V.
  full_name: Seidel, Julia V.
  last_name: Seidel
- first_name: H. Jens
  full_name: Hoeijmakers, H. Jens
  last_name: Hoeijmakers
- first_name: Athira
  full_name: Unni, Athira
  last_name: Unni
- first_name: Aurora Y.
  full_name: Kesseli, Aurora Y.
  last_name: Kesseli
- first_name: Carl A.
  full_name: Schmidt, Carl A.
  last_name: Schmidt
- first_name: Thirupathi
  full_name: Sivarani, Thirupathi
  last_name: Sivarani
- first_name: Aaron
  full_name: Bello-Arufe, Aaron
  last_name: Bello-Arufe
- first_name: Andrea
  full_name: Gebek, Andrea
  last_name: Gebek
- first_name: Moritz
  full_name: Meyer Zu Westram, Moritz
  last_name: Meyer Zu Westram
- first_name: Sérgio G.
  full_name: Sousa, Sérgio G.
  last_name: Sousa
- first_name: Rosaly M.C.
  full_name: Lopes, Rosaly M.C.
  last_name: Lopes
- first_name: Renyu
  full_name: Hu, Renyu
  last_name: Hu
- first_name: Katherine
  full_name: De Kleer, Katherine
  last_name: De Kleer
- first_name: Chloe
  full_name: Fisher, Chloe
  last_name: Fisher
- first_name: Sébastien
  full_name: Charnoz, Sébastien
  last_name: Charnoz
- first_name: Ashley D.
  full_name: Baker, Ashley D.
  last_name: Baker
- first_name: Samuel P.
  full_name: Halverson, Samuel P.
  last_name: Halverson
- first_name: Nick M.
  full_name: Schneider, Nick M.
  last_name: Schneider
- first_name: Angelica
  full_name: Psaridi, Angelica
  last_name: Psaridi
- first_name: Aurélien
  full_name: Wyttenbach, Aurélien
  last_name: Wyttenbach
- first_name: Santiago
  full_name: Torres Rodriguez, Santiago
  id: a8df4360-4328-11ee-8f1a-e502d0c83fc2
  last_name: Torres Rodriguez
  orcid: 0000-0002-3150-8988
- first_name: Ishita
  full_name: Bhatnagar, Ishita
  last_name: Bhatnagar
- first_name: Robert E.
  full_name: Johnson, Robert E.
  last_name: Johnson
citation:
  ama: Oza AV, Seidel JV, Hoeijmakers HJ, et al. Redshifted sodium transient near
    exoplanet transit. <i>Astrophysical Journal Letters</i>. 2024;973(2). doi:<a href="https://doi.org/10.3847/2041-8213/ad6b29">10.3847/2041-8213/ad6b29</a>
  apa: Oza, A. V., Seidel, J. V., Hoeijmakers, H. J., Unni, A., Kesseli, A. Y., Schmidt,
    C. A., … Johnson, R. E. (2024). Redshifted sodium transient near exoplanet transit.
    <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href="https://doi.org/10.3847/2041-8213/ad6b29">https://doi.org/10.3847/2041-8213/ad6b29</a>
  chicago: Oza, Apurva V., Julia V. Seidel, H. Jens Hoeijmakers, Athira Unni, Aurora
    Y. Kesseli, Carl A. Schmidt, Thirupathi Sivarani, et al. “Redshifted Sodium Transient
    near Exoplanet Transit.” <i>Astrophysical Journal Letters</i>. IOP Publishing,
    2024. <a href="https://doi.org/10.3847/2041-8213/ad6b29">https://doi.org/10.3847/2041-8213/ad6b29</a>.
  ieee: A. V. Oza <i>et al.</i>, “Redshifted sodium transient near exoplanet transit,”
    <i>Astrophysical Journal Letters</i>, vol. 973, no. 2. IOP Publishing, 2024.
  ista: Oza AV, Seidel JV, Hoeijmakers HJ, Unni A, Kesseli AY, Schmidt CA, Sivarani
    T, Bello-Arufe A, Gebek A, Meyer Zu Westram M, Sousa SG, Lopes RMC, Hu R, De Kleer
    K, Fisher C, Charnoz S, Baker AD, Halverson SP, Schneider NM, Psaridi A, Wyttenbach
    A, Torres Rodriguez S, Bhatnagar I, Johnson RE. 2024. Redshifted sodium transient
    near exoplanet transit. Astrophysical Journal Letters. 973(2), L53.
  mla: Oza, Apurva V., et al. “Redshifted Sodium Transient near Exoplanet Transit.”
    <i>Astrophysical Journal Letters</i>, vol. 973, no. 2, L53, IOP Publishing, 2024,
    doi:<a href="https://doi.org/10.3847/2041-8213/ad6b29">10.3847/2041-8213/ad6b29</a>.
  short: A.V. Oza, J.V. Seidel, H.J. Hoeijmakers, A. Unni, A.Y. Kesseli, C.A. Schmidt,
    T. Sivarani, A. Bello-Arufe, A. Gebek, M. Meyer Zu Westram, S.G. Sousa, R.M.C.
    Lopes, R. Hu, K. De Kleer, C. Fisher, S. Charnoz, A.D. Baker, S.P. Halverson,
    N.M. Schneider, A. Psaridi, A. Wyttenbach, S. Torres Rodriguez, I. Bhatnagar,
    R.E. Johnson, Astrophysical Journal Letters 973 (2024).
date_created: 2024-10-13T22:01:49Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-08T14:18:18Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.3847/2041-8213/ad6b29
external_id:
  arxiv:
  - '2409.19844'
  isi:
  - '001322169500001'
file:
- access_level: open_access
  checksum: 23eea2a6a0519694a84998957ad7b7fb
  content_type: application/pdf
  creator: dernst
  date_created: 2024-10-21T11:05:11Z
  date_updated: 2024-10-21T11:05:11Z
  file_id: '18456'
  file_name: 2024_AstrophysicalJourn_Oza.pdf
  file_size: 1249747
  relation: main_file
  success: 1
file_date_updated: 2024-10-21T11:05:11Z
has_accepted_license: '1'
intvolume: '       973'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Astrophysical Journal Letters
publication_identifier:
  eissn:
  - 2041-8213
  issn:
  - 2041-8205
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Redshifted sodium transient near exoplanet transit
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: 973
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18308'
abstract:
- lang: eng
  text: We study in this paper the problem of maintaining a solution to k-median and
    k-means clustering in a fully dynamic setting. To do so, we present an algorithm
    to efficiently maintain a coreset, a compressed version of the dataset, that allows
    easy computation of a clustering solution at query time. Our coreset algorithm
    has near-optimal update time of Õ(k) in general metric spaces, which reduces to
    Õ(d) in the Euclidean space ℝ^d. The query time is O(k²) in general metrics, and
    O(kd) in ℝ^d. To maintain a constant-factor approximation for k-median and k-means
    clustering in Euclidean space, this directly leads to an algorithm with update
    time Õ(d), and query time Õ(kd + k²). To maintain a O(polylog k)-approximation,
    the query time is reduced to Õ(kd).
acknowledgement: "Monika Henzinger: This project has received funding from the European
  Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
  programme (MoDynStruct Grant agreement No. 101019564) and the Austrian Science Fund
  (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775
  with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nDavid Saulpic:
  Work partially done while at ISTA. Received funding from the European Union’s\r\nHorizon
  2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement
  No 101034413. This work was partially funded by the grant ANR-19-CE48-0016 from
  the French National Research Agency (ANR)."
alternative_title:
- LIPIcs
article_number: '100'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Max Dupré
  full_name: La Tour, Max Dupré
  last_name: La Tour
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: David
  full_name: Saulpic, David
  id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964
  last_name: Saulpic
citation:
  ama: 'La Tour MD, Henzinger M, Saulpic D. Fully dynamic k-means coreset in near-optimal
    update time. In: <i>32nd Annual European Symposium on Algorithms</i>. Vol 308.
    Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href="https://doi.org/10.4230/LIPIcs.ESA.2024.100">10.4230/LIPIcs.ESA.2024.100</a>'
  apa: 'La Tour, M. D., Henzinger, M., &#38; Saulpic, D. (2024). Fully dynamic k-means
    coreset in near-optimal update time. In <i>32nd Annual European Symposium on Algorithms</i>
    (Vol. 308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
    <a href="https://doi.org/10.4230/LIPIcs.ESA.2024.100">https://doi.org/10.4230/LIPIcs.ESA.2024.100</a>'
  chicago: La Tour, Max Dupré, Monika Henzinger, and David Saulpic. “Fully Dynamic
    K-Means Coreset in near-Optimal Update Time.” In <i>32nd Annual European Symposium
    on Algorithms</i>, Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2024. <a href="https://doi.org/10.4230/LIPIcs.ESA.2024.100">https://doi.org/10.4230/LIPIcs.ESA.2024.100</a>.
  ieee: M. D. La Tour, M. Henzinger, and D. Saulpic, “Fully dynamic k-means coreset
    in near-optimal update time,” in <i>32nd Annual European Symposium on Algorithms</i>,
    London, United Kingdom, 2024, vol. 308.
  ista: 'La Tour MD, Henzinger M, Saulpic D. 2024. Fully dynamic k-means coreset in
    near-optimal update time. 32nd Annual European Symposium on Algorithms. ESA: European
    Symposium on Algorithms, LIPIcs, vol. 308, 100.'
  mla: La Tour, Max Dupré, et al. “Fully Dynamic K-Means Coreset in near-Optimal Update
    Time.” <i>32nd Annual European Symposium on Algorithms</i>, vol. 308, 100, Schloss
    Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href="https://doi.org/10.4230/LIPIcs.ESA.2024.100">10.4230/LIPIcs.ESA.2024.100</a>.
  short: M.D. La Tour, M. Henzinger, D. Saulpic, in:, 32nd Annual European Symposium
    on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
  end_date: 2024-09-04
  location: London, United Kingdom
  name: 'ESA: European Symposium on Algorithms'
  start_date: 2024-09-02
corr_author: '1'
date_created: 2024-10-13T22:01:50Z
date_published: 2024-09-23T00:00:00Z
date_updated: 2025-12-02T13:49:11Z
day: '23'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ESA.2024.100
ec_funded: 1
external_id:
  arxiv:
  - '2406.19926'
  isi:
  - '001545622400100'
file:
- access_level: open_access
  checksum: 8e8c0b13049f11bb0133dfac22e32718
  content_type: application/pdf
  creator: dernst
  date_created: 2024-10-21T09:41:48Z
  date_updated: 2024-10-21T09:41:48Z
  file_id: '18454'
  file_name: 2024_LIPICs_DuprelaTour.pdf
  file_size: 873561
  relation: main_file
  success: 1
file_date_updated: 2024-10-21T09:41:48Z
has_accepted_license: '1'
intvolume: '       308'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
  call_identifier: H2020
  grant_number: '101019564'
  name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
  grant_number: Z00422
  name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
  grant_number: I05982
  name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
  grant_number: P33775
  name: Fast Algorithms for a Reactive Network Layer
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: 32nd Annual European Symposium on Algorithms
publication_identifier:
  isbn:
  - '9783959773386'
  issn:
  - 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fully dynamic k-means coreset in near-optimal update time
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 308
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18309'
abstract:
- lang: eng
  text: 'The problem of designing connectivity oracles supporting vertex failures
    is one of the basic data structures problems for undirected graphs. It is already
    well understood: previous works [Duan-Pettie STOC''10; Long-Saranurak FOCS''22]
    achieve query time linear in the number of failed vertices, and it is conditionally
    optimal as long as we require preprocessing time polynomial in the size of the
    graph and update time polynomial in the number of failed vertices. We revisit
    this problem in the paradigm of algorithms with predictions: we ask if the query
    time can be improved if the set of failed vertices can be predicted beforehand
    up to a small number of errors. More specifically, we design a data structure
    that, given a graph G = (V,E) and a set of vertices predicted to fail D̂ ⊆ V of
    size d = |D̂|, preprocesses it in time Õ(d|E|) and then can receive an update
    given as the symmetric difference between the predicted and the actual set of
    failed vertices D̂△D = (D̂ ⧵ D) ∪ (D ⧵ D̂) of size η = |D̂△D|, process it in time
    Õ(η⁴), and after that answer connectivity queries in G ⧵ D in time O(η). Viewed
    from another perspective, our data structure provides an improvement over the
    state of the art for the fully dynamic subgraph connectivity problem in the sensitivity
    setting [Henzinger-Neumann ESA''16]. We argue that the preprocessing time and
    query time of our data structure are conditionally optimal under standard fine-grained
    complexity assumptions.'
acknowledgement: "Part of this work was done when Evangelos Kosinas was at University
  of Ioannina and Adam Polak was at Max Planck Institute of Informatics.\r\n"
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Bingbing
  full_name: Hu, Bingbing
  last_name: Hu
- first_name: Evangelos
  full_name: Kosinas, Evangelos
  id: 4c7f9625-dbbc-11ee-9d86-bdcc2db5a949
  last_name: Kosinas
- first_name: Adam
  full_name: Polak, Adam
  last_name: Polak
citation:
  ama: 'Hu B, Kosinas E, Polak A. Connectivity oracles for predictable vertex failures.
    In: <i>32nd Annual European Symposium on Algorithms</i>. Vol 308. Schloss Dagstuhl
    - Leibniz-Zentrum für Informatik; 2024. doi:<a href="https://doi.org/10.4230/LIPIcs.ESA.2024.72">10.4230/LIPIcs.ESA.2024.72</a>'
  apa: 'Hu, B., Kosinas, E., &#38; Polak, A. (2024). Connectivity oracles for predictable
    vertex failures. In <i>32nd Annual European Symposium on Algorithms</i> (Vol.
    308). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
    <a href="https://doi.org/10.4230/LIPIcs.ESA.2024.72">https://doi.org/10.4230/LIPIcs.ESA.2024.72</a>'
  chicago: Hu, Bingbing, Evangelos Kosinas, and Adam Polak. “Connectivity Oracles
    for Predictable Vertex Failures.” In <i>32nd Annual European Symposium on Algorithms</i>,
    Vol. 308. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href="https://doi.org/10.4230/LIPIcs.ESA.2024.72">https://doi.org/10.4230/LIPIcs.ESA.2024.72</a>.
  ieee: B. Hu, E. Kosinas, and A. Polak, “Connectivity oracles for predictable vertex
    failures,” in <i>32nd Annual European Symposium on Algorithms</i>, London, United
    Kingdom, 2024, vol. 308.
  ista: 'Hu B, Kosinas E, Polak A. 2024. Connectivity oracles for predictable vertex
    failures. 32nd Annual European Symposium on Algorithms. ESA: European Symposium
    on Algorithms, LIPIcs, vol. 308, 72.'
  mla: Hu, Bingbing, et al. “Connectivity Oracles for Predictable Vertex Failures.”
    <i>32nd Annual European Symposium on Algorithms</i>, vol. 308, 72, Schloss Dagstuhl
    - Leibniz-Zentrum für Informatik, 2024, doi:<a href="https://doi.org/10.4230/LIPIcs.ESA.2024.72">10.4230/LIPIcs.ESA.2024.72</a>.
  short: B. Hu, E. Kosinas, A. Polak, in:, 32nd Annual European Symposium on Algorithms,
    Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
  end_date: 2024-09-04
  location: London, United Kingdom
  name: 'ESA: European Symposium on Algorithms'
  start_date: 2024-09-02
corr_author: '1'
date_created: 2024-10-13T22:01:50Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-12-02T13:49:52Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ESA.2024.72
external_id:
  arxiv:
  - '2312.08489'
  isi:
  - '001545622400072'
file:
- access_level: open_access
  checksum: ab1f2f9161549a8763eda15db40e022c
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  creator: dernst
  date_created: 2024-10-21T10:03:48Z
  date_updated: 2024-10-21T10:03:48Z
  file_id: '18455'
  file_name: 2024_LIPICs_Hu.pdf
  file_size: 853914
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  success: 1
file_date_updated: 2024-10-21T10:03:48Z
has_accepted_license: '1'
intvolume: '       308'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: 32nd Annual European Symposium on Algorithms
publication_identifier:
  isbn:
  - '9783959773386'
  issn:
  - 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connectivity oracles for predictable vertex failures
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 308
year: '2024'
...
---
OA_type: closed access
_id: '18310'
article_processing_charge: No
article_type: original
author:
- first_name: Maria
  full_name: Kitsara, Maria
  last_name: Kitsara
- first_name: Merima
  full_name: Smajlhodžić-Deljo, Merima
  last_name: Smajlhodžić-Deljo
- first_name: Lejla
  full_name: Gurbeta Pokvic, Lejla
  last_name: Gurbeta Pokvic
- first_name: Bettina
  full_name: Bert, Bettina
  last_name: Bert
- first_name: Nataliia
  full_name: Bubalo, Nataliia
  last_name: Bubalo
- first_name: Sevilay
  full_name: Erden, Sevilay
  last_name: Erden
- first_name: Nuno Henrique
  full_name: Franco, Nuno Henrique
  last_name: Franco
- first_name: Giuseppe
  full_name: Chirico, Giuseppe
  last_name: Chirico
- first_name: Jonathan
  full_name: Gómez Raja, Jonathan
  last_name: Gómez Raja
- first_name: Fernando
  full_name: Gonzalez-Uarquin, Fernando
  last_name: Gonzalez-Uarquin
- first_name: Annemarie
  full_name: Lang, Annemarie
  last_name: Lang
- first_name: Nicole
  full_name: Linklater, Nicole
  last_name: Linklater
- first_name: Sandra
  full_name: Mojsova, Sandra
  last_name: Mojsova
- first_name: I. Anna S.
  full_name: Olsson, I. Anna S.
  last_name: Olsson
- first_name: Ioanna
  full_name: Sandvig, Ioanna
  last_name: Sandvig
- first_name: Alexandra
  full_name: Schaffert, Alexandra
  last_name: Schaffert
- first_name: Marthe
  full_name: Schmit, Marthe
  last_name: Schmit
- first_name: Sophie
  full_name: Schober, Sophie
  id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8
  last_name: Schober
- first_name: Bogdan
  full_name: Sevastre, Bogdan
  last_name: Sevastre
- first_name: Doris
  full_name: Wilflingseder, Doris
  last_name: Wilflingseder
- first_name: Arti
  full_name: Ahluwalia, Arti
  last_name: Ahluwalia
- first_name: Winfried
  full_name: Neuhaus, Winfried
  last_name: Neuhaus
citation:
  ama: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, et al. Introducing the COST
    action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE).
    <i>Alternatives to Laboratory Animals</i>. 2024;52(6):326-333. doi:<a href="https://doi.org/10.1177/02611929241286024">10.1177/02611929241286024</a>
  apa: Kitsara, M., Smajlhodžić-Deljo, M., Gurbeta Pokvic, L., Bert, B., Bubalo, N.,
    Erden, S., … Neuhaus, W. (2024). Introducing the COST action ‘Improving the Quality
    of Biomedical Science with 3Rs Concepts’ (IMPROVE). <i>Alternatives to Laboratory
    Animals</i>. SAGE Publications. <a href="https://doi.org/10.1177/02611929241286024">https://doi.org/10.1177/02611929241286024</a>
  chicago: Kitsara, Maria, Merima Smajlhodžić-Deljo, Lejla Gurbeta Pokvic, Bettina
    Bert, Nataliia Bubalo, Sevilay Erden, Nuno Henrique Franco, et al. “Introducing
    the COST Action ‘Improving the Quality of Biomedical Science with 3Rs Concepts’
    (IMPROVE).” <i>Alternatives to Laboratory Animals</i>. SAGE Publications, 2024.
    <a href="https://doi.org/10.1177/02611929241286024">https://doi.org/10.1177/02611929241286024</a>.
  ieee: M. Kitsara <i>et al.</i>, “Introducing the COST action ‘Improving the Quality
    of Biomedical Science with 3Rs Concepts’ (IMPROVE),” <i>Alternatives to Laboratory
    Animals</i>, vol. 52, no. 6. SAGE Publications, pp. 326–333, 2024.
  ista: Kitsara M, Smajlhodžić-Deljo M, Gurbeta Pokvic L, Bert B, Bubalo N, Erden
    S, Franco NH, Chirico G, Gómez Raja J, Gonzalez-Uarquin F, Lang A, Linklater N,
    Mojsova S, Olsson IAS, Sandvig I, Schaffert A, Schmit M, Schober S, Sevastre B,
    Wilflingseder D, Ahluwalia A, Neuhaus W. 2024. Introducing the COST action ‘Improving
    the Quality of Biomedical Science with 3Rs Concepts’ (IMPROVE). Alternatives to
    Laboratory Animals. 52(6), 326–333.
  mla: Kitsara, Maria, et al. “Introducing the COST Action ‘Improving the Quality
    of Biomedical Science with 3Rs Concepts’ (IMPROVE).” <i>Alternatives to Laboratory
    Animals</i>, vol. 52, no. 6, SAGE Publications, 2024, pp. 326–33, doi:<a href="https://doi.org/10.1177/02611929241286024">10.1177/02611929241286024</a>.
  short: M. Kitsara, M. Smajlhodžić-Deljo, L. Gurbeta Pokvic, B. Bert, N. Bubalo,
    S. Erden, N.H. Franco, G. Chirico, J. Gómez Raja, F. Gonzalez-Uarquin, A. Lang,
    N. Linklater, S. Mojsova, I.A.S. Olsson, I. Sandvig, A. Schaffert, M. Schmit,
    S. Schober, B. Sevastre, D. Wilflingseder, A. Ahluwalia, W. Neuhaus, Alternatives
    to Laboratory Animals 52 (2024) 326–333.
date_created: 2024-10-13T22:01:51Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-08T09:56:39Z
day: '01'
department:
- _id: PreCl
doi: 10.1177/02611929241286024
external_id:
  isi:
  - '001348633700007'
  pmid:
  - '39333027'
intvolume: '        52'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 326-333
pmid: 1
publication: Alternatives to Laboratory Animals
publication_identifier:
  eissn:
  - 2632-3559
  issn:
  - 0261-1929
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introducing the COST action ‘Improving the Quality of Biomedical Science with
  3Rs Concepts’ (IMPROVE)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 52
year: '2024'
...
---
OA_type: closed access
_id: '18311'
abstract:
- lang: eng
  text: Local wound signaling in plants informs the surrounding tissues about an injury
    and initiates the regeneration process. In a recent paper published in Cell, Yang
    and colleagues show the involvement of a single Pep family member from tomato
    in wound signaling and how exogenous application of this regeneration factor enhances
    transformation efficiency in crops.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
  full_name: Hörmayer, Lukas
  id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
  last_name: Hörmayer
  orcid: 0000-0001-8295-2926
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: 'Hörmayer L, Friml J. Feeling the danger: Local wound signaling in plants.
    <i>Cell Research</i>. 2024;34:761-762. doi:<a href="https://doi.org/10.1038/s41422-024-01035-x">10.1038/s41422-024-01035-x</a>'
  apa: 'Hörmayer, L., &#38; Friml, J. (2024). Feeling the danger: Local wound signaling
    in plants. <i>Cell Research</i>. Springer Nature. <a href="https://doi.org/10.1038/s41422-024-01035-x">https://doi.org/10.1038/s41422-024-01035-x</a>'
  chicago: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling
    in Plants.” <i>Cell Research</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s41422-024-01035-x">https://doi.org/10.1038/s41422-024-01035-x</a>.'
  ieee: 'L. Hörmayer and J. Friml, “Feeling the danger: Local wound signaling in plants,”
    <i>Cell Research</i>, vol. 34. Springer Nature, pp. 761–762, 2024.'
  ista: 'Hörmayer L, Friml J. 2024. Feeling the danger: Local wound signaling in plants.
    Cell Research. 34, 761–762.'
  mla: 'Hörmayer, Lukas, and Jiří Friml. “Feeling the Danger: Local Wound Signaling
    in Plants.” <i>Cell Research</i>, vol. 34, Springer Nature, 2024, pp. 761–62,
    doi:<a href="https://doi.org/10.1038/s41422-024-01035-x">10.1038/s41422-024-01035-x</a>.'
  short: L. Hörmayer, J. Friml, Cell Research 34 (2024) 761–762.
corr_author: '1'
date_created: 2024-10-13T22:01:51Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-08T09:57:18Z
day: '01'
department:
- _id: JiFr
doi: 10.1038/s41422-024-01035-x
external_id:
  isi:
  - '001326684200001'
  pmid:
  - '39354142'
intvolume: '        34'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
page: 761-762
pmid: 1
publication: Cell Research
publication_identifier:
  eissn:
  - 1748-7838
  issn:
  - 1001-0602
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Feeling the danger: Local wound signaling in plants'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 34
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18445'
abstract:
- lang: eng
  text: Acquisition of specialized cellular features is controlled by the ordered
    expression of transcription factors (TFs) along differentiation trajectories.
    Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic
    neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate
    hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq
    and gain-of-function experiments for gene network reconstruction to show that
    ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived
    dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron
    navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice
    reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons,
    while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring,
    and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal
    subtypes and many species, underpins the polarization and morphological plasticity
    of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors
    in the hypothalamus.
acknowledgement: "The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom
  generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all
  from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest,
  Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility,
  Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral
  Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for
  providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher
  (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit
  bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms
  and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical
  Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged
  for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical
  University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and
  W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their
  technical assistance. C. elegans strains were provided by the National Bioresource
  Project for the nematode, Japan, and the CGC, with the latter being funded by the
  NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported
  by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council
  (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden,
  FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.),
  the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the
  Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and
  Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21,
  to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported
  by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L).
  E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research
  Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska
  Institute."
article_number: '8631'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Maja
  full_name: Zupančič, Maja
  last_name: Zupančič
- first_name: Erik
  full_name: Keimpema, Erik
  last_name: Keimpema
- first_name: Evgenii O.
  full_name: Tretiakov, Evgenii O.
  last_name: Tretiakov
- first_name: Stephanie J.
  full_name: Eder, Stephanie J.
  last_name: Eder
- first_name: Itamar
  full_name: Lev, Itamar
  last_name: Lev
- first_name: Lukas
  full_name: Englmaier, Lukas
  last_name: Englmaier
- first_name: Pradeep
  full_name: Bhandari, Pradeep
  id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
  last_name: Bhandari
  orcid: 0000-0003-0863-4481
- first_name: Simone A.
  full_name: Fietz, Simone A.
  last_name: Fietz
- first_name: Wolfgang
  full_name: Härtig, Wolfgang
  last_name: Härtig
- first_name: Estelle
  full_name: Renaux, Estelle
  last_name: Renaux
- first_name: Andreas
  full_name: Villunger, Andreas
  last_name: Villunger
- first_name: Tomas
  full_name: Hökfelt, Tomas
  last_name: Hökfelt
- first_name: Manuel
  full_name: Zimmer, Manuel
  last_name: Zimmer
- first_name: Frédéric
  full_name: Clotman, Frédéric
  last_name: Clotman
- first_name: Tibor
  full_name: Harkany, Tibor
  last_name: Harkany
citation:
  ama: Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation
    of the morphogenesis of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>.
    2024;15. doi:<a href="https://doi.org/10.1038/s41467-024-52762-z">10.1038/s41467-024-52762-z</a>
  apa: Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier,
    L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis
    of hypothalamic neurons by ONECUT3. <i>Nature Communications</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41467-024-52762-z">https://doi.org/10.1038/s41467-024-52762-z</a>
  chicago: Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder,
    Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional
    Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” <i>Nature
    Communications</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s41467-024-52762-z">https://doi.org/10.1038/s41467-024-52762-z</a>.
  ieee: M. Zupančič <i>et al.</i>, “Concerted transcriptional regulation of the morphogenesis
    of hypothalamic neurons by ONECUT3,” <i>Nature Communications</i>, vol. 15. Springer
    Nature, 2024.
  ista: Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari
    P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F,
    Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of
    hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.
  mla: Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis
    of Hypothalamic Neurons by ONECUT3.” <i>Nature Communications</i>, vol. 15, 8631,
    Springer Nature, 2024, doi:<a href="https://doi.org/10.1038/s41467-024-52762-z">10.1038/s41467-024-52762-z</a>.
  short: M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier,
    P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer,
    F. Clotman, T. Harkany, Nature Communications 15 (2024).
date_created: 2024-10-20T22:02:05Z
date_published: 2024-10-05T00:00:00Z
date_updated: 2025-09-08T14:25:06Z
day: '05'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1038/s41467-024-52762-z
external_id:
  isi:
  - '001409493300014'
  pmid:
  - '39366958'
file:
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  creator: dernst
  date_created: 2024-10-21T12:15:38Z
  date_updated: 2024-10-21T12:15:38Z
  file_id: '18460'
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month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons
  by ONECUT3
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: 15
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18446'
abstract:
- lang: eng
  text: How living systems achieve precision in form and function despite their intrinsic
    stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps
    of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these
    morphomaps revealed that although blastomere divisions desynchronized passively,
    8-cell embryos converged toward robust three-dimensional shapes. Using topological
    analysis and genetic perturbations, we found that embryos progressively changed
    their cellular connectivity to a preferred topology, which could be predicted
    by a physical model in which actomyosin contractility and noise facilitate topological
    transitions, lowering surface energy. This mechanism favored regular embryo packing
    and promoted a higher number of inner cells in the 16-cell embryo. Synchronized
    division reduced embryo packing and generated substantially more misallocated
    cells and fewer inner-cell–mass cells. These findings suggest that stochasticity
    in division timing contributes to robust patterning.
acknowledgement: "We are grateful to the members of the Hiiragi laboratory for discussions
  and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and
  W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol;
  members of the Tsukiyama group for the animal care with monkeys, in particular H.
  Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas,
  France) for the animal care with rabbits; the EMBL electronic and mechanical workshops
  and the EMBL animal facility for their support; We thank Luxendo for the close collaboration
  in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This
  work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD)
  under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research
  Fellowship (to T.I.); Field of excellence “Complexity of life in basic research
  and innovation” of the University of Graz (to B.C.M.); European Research Council,
  ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced
  Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant
  LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)"
article_number: eadh1145
article_processing_charge: No
article_type: original
author:
- first_name: Dimitri
  full_name: Fabrèges, Dimitri
  last_name: Fabrèges
- first_name: Bernat
  full_name: Corominas-Murtra, Bernat
  id: 43BE2298-F248-11E8-B48F-1D18A9856A87
  last_name: Corominas-Murtra
  orcid: 0000-0001-9806-5643
- first_name: Prachiti
  full_name: Moghe, Prachiti
  last_name: Moghe
- first_name: Alison
  full_name: Kickuth, Alison
  last_name: Kickuth
- first_name: Takafumi
  full_name: Ichikawa, Takafumi
  last_name: Ichikawa
- first_name: Chizuru
  full_name: Iwatani, Chizuru
  last_name: Iwatani
- first_name: Tomoyuki
  full_name: Tsukiyama, Tomoyuki
  last_name: Tsukiyama
- first_name: Nathalie
  full_name: Daniel, Nathalie
  last_name: Daniel
- first_name: Julie
  full_name: Gering, Julie
  last_name: Gering
- first_name: Anniek
  full_name: Stokkermans, Anniek
  last_name: Stokkermans
- first_name: Adrian
  full_name: Wolny, Adrian
  last_name: Wolny
- first_name: Anna
  full_name: Kreshuk, Anna
  last_name: Kreshuk
- first_name: Véronique
  full_name: Duranthon, Véronique
  last_name: Duranthon
- first_name: Virginie
  full_name: Uhlman, Virginie
  last_name: Uhlman
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
- first_name: Takashi
  full_name: Hiiragi, Takashi
  last_name: Hiiragi
citation:
  ama: Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell
    mechanics control robustness in mammalian embryogenesis. <i>Science</i>. 2024;386(6718).
    doi:<a href="https://doi.org/10.1126/science.adh1145">10.1126/science.adh1145</a>
  apa: Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani,
    C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness
    in mammalian embryogenesis. <i>Science</i>. AAAS. <a href="https://doi.org/10.1126/science.adh1145">https://doi.org/10.1126/science.adh1145</a>
  chicago: Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth,
    Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability
    and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” <i>Science</i>.
    AAAS, 2024. <a href="https://doi.org/10.1126/science.adh1145">https://doi.org/10.1126/science.adh1145</a>.
  ieee: D. Fabrèges <i>et al.</i>, “Temporal variability and cell mechanics control
    robustness in mammalian embryogenesis,” <i>Science</i>, vol. 386, no. 6718. AAAS,
    2024.
  ista: Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C,
    Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon
    V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics
    control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.
  mla: Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control
    Robustness in Mammalian Embryogenesis.” <i>Science</i>, vol. 386, no. 6718, eadh1145,
    AAAS, 2024, doi:<a href="https://doi.org/10.1126/science.adh1145">10.1126/science.adh1145</a>.
  short: D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani,
    T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon,
    V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).
corr_author: '1'
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2025-09-08T14:22:13Z
day: '11'
department:
- _id: EdHa
doi: 10.1126/science.adh1145
external_id:
  isi:
  - '001422132300018'
  pmid:
  - '39388574'
intvolume: '       386'
isi: 1
issue: '6718'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Temporal variability and cell mechanics control robustness in mammalian embryogenesis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 386
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18447'
abstract:
- lang: eng
  text: We present the first results on the spatial distribution of star formation
    in 454 star-forming galaxies just after the epoch of reionisation (4.8 < z < 6.5)
    using Hα emission-line maps and F444W imaging that traces the stellar continuum
    from the JWST FRESCO NIRCam Slitless Spectroscopy Survey. The Hα equivalent width
    profiles of star-forming galaxies across the main sequence at z ∼ 5.3 with stellar
    masses 6.8≤ log(M*/M⊙) < 11.1 increase with radius, which provides direct evidence
    for the inside-out growth of star-forming galaxies just after the epoch of reionisation.
    GALFIT was used to calculate half-light radii, Reff, and central surface densities
    within 1 kiloparsec, Σ1kpc of Hα and the continuum. At a fixed stellar mass of
    Log(M*/M⊙) = 9.5, Σ1kpc, Hα is 1.04 ± 0.05 times higher than Σ1kpc, C, Reff, Hα
    is 1.18 ± 0.03 times larger than Reff, C and both Reff measurements are smaller
    than 1 kiloparsec. These measurements suggest the rapid build-up of compact bulges
    via star formation just after the epoch of reionisation. By comparison to analogous
    work done at lower redshifts with Hubble Space Telescope WFC3 slitless spectroscopy
    as part of the 3D-HST (z ∼ 1) and CLEAR (z ∼ 0.5) surveys, we find that Reff(z)
    evolves at the same pace for Hα and the continuum, but Σ1kpc(z) evolves faster
    for Hα than the stellar continuum. As a function of the Hubble parameter, Reff, Hα/Reff,C = 1.1h(z)
    and Σ1 kpc, Hα/Σ1 kpc,C = h(z)1.3. These parametrisations suggest that the inside-out
    growth of the disk starts to dominate the inside-out growth of the bulge towards
    lower redshifts. This is supported by the redshift evolution in the EW(Hα) profiles
    from FRESCO, 3D-HST, and CLEAR at fixed stellar mass and when star-forming progenitors
    are traced, in which in EW(Hα) rapidly increases with radius within the half-light
    radius at z ∼ 5.3, but EW(Hα) increases only significantly with radius in the
    outer disk at z ∼ 0.5.
acknowledgement: "JM is grateful to the Cosmic Dawn Center for the DAWN Fellowship.
  JM thanks Adam Muzzin, Viola Gelli and Anne Hutter for useful discussions that led
  to improvements in the analysis presented in this paper. This work is based on observations
  made with the NASA/ESA/CSA James Webb Space Telescope. The raw data were obtained
  from the Mikulski Archive for\r\nSpace Telescopes at the Space Telescope Science
  Institute, which is operated by the Association of Universities for Research in
  Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are
  associated with JWST Cycle 1 GO program #1895. Support for program JWST-GO-1895
  was provided by NASA through a grant from the Space Telescope Science Institute,
  which is operated by the Associations of Universities for Research in Astronomy,
  Incorporated, under NASA contract NAS5-26555. The Cosmic Dawn Center  DAWN) is funded
  by the Danish National Research Foundation under grant DNRF140.\r\nThis work has
  received funding from the Swiss State Secretariat for Education, Research and Innovation
  (SERI) under contract number MB22.00072, as well as from the Swiss National Science
  Foundation (SNSF) through project grant 200020_207349. RPN thanks the NASA Hubble
  Fellowshp Program for the Hubble Fellowship. DM acknowledges funding from JWST-GO-01895.013,
  provided through a grant from the STScI under NASA contract NAS5-03127."
article_number: A64
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Jasleen
  full_name: Matharu, Jasleen
  last_name: Matharu
- first_name: Erica J.
  full_name: Nelson, Erica J.
  last_name: Nelson
- first_name: Gabriel
  full_name: Brammer, Gabriel
  last_name: Brammer
- first_name: Pascal A.
  full_name: Oesch, Pascal A.
  last_name: Oesch
- first_name: Natalie
  full_name: Allen, Natalie
  last_name: Allen
- first_name: Irene
  full_name: Shivaei, Irene
  last_name: Shivaei
- first_name: Rohan P.
  full_name: Naidu, Rohan P.
  last_name: Naidu
- first_name: John
  full_name: Chisholm, John
  last_name: Chisholm
- first_name: Alba
  full_name: Covelo-Paz, Alba
  last_name: Covelo-Paz
- first_name: Yoshinobu
  full_name: Fudamoto, Yoshinobu
  last_name: Fudamoto
- first_name: Emma
  full_name: Giovinazzo, Emma
  last_name: Giovinazzo
- first_name: Thomas
  full_name: Herard-Demanche, Thomas
  last_name: Herard-Demanche
- first_name: Josephine
  full_name: Kerutt, Josephine
  last_name: Kerutt
- first_name: Ivan
  full_name: Kramarenko, Ivan
  id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4
  last_name: Kramarenko
  orcid: 0000-0001-5346-6048
- first_name: Danilo
  full_name: Marchesini, Danilo
  last_name: Marchesini
- first_name: Romain A.
  full_name: Meyer, Romain A.
  last_name: Meyer
- first_name: Gonzalo
  full_name: Prieto-Lyon, Gonzalo
  last_name: Prieto-Lyon
- first_name: Naveen
  full_name: Reddy, Naveen
  last_name: Reddy
- first_name: Marko
  full_name: Shuntov, Marko
  last_name: Shuntov
- first_name: Andrea
  full_name: Weibel, Andrea
  last_name: Weibel
- first_name: Stijn
  full_name: Wuyts, Stijn
  last_name: Wuyts
- first_name: Mengyuan
  full_name: Xiao, Mengyuan
  last_name: Xiao
citation:
  ama: Matharu J, Nelson EJ, Brammer G, et al. A first look at spatially resolved
    star formation at 4.8 &#60; z &#60; 6.5 with JWST FRESCO NIRCam slitless spectroscopy.
    <i>Astronomy and Astrophysics</i>. 2024;690. doi:<a href="https://doi.org/10.1051/0004-6361/202450522">10.1051/0004-6361/202450522</a>
  apa: Matharu, J., Nelson, E. J., Brammer, G., Oesch, P. A., Allen, N., Shivaei,
    I., … Xiao, M. (2024). A first look at spatially resolved star formation at 4.8
    &#60; z &#60; 6.5 with JWST FRESCO NIRCam slitless spectroscopy. <i>Astronomy
    and Astrophysics</i>. EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/202450522">https://doi.org/10.1051/0004-6361/202450522</a>
  chicago: Matharu, Jasleen, Erica J. Nelson, Gabriel Brammer, Pascal A. Oesch, Natalie
    Allen, Irene Shivaei, Rohan P. Naidu, et al. “A First Look at Spatially Resolved
    Star Formation at 4.8 &#60; z &#60; 6.5 with JWST FRESCO NIRCam Slitless Spectroscopy.”
    <i>Astronomy and Astrophysics</i>. EDP Sciences, 2024. <a href="https://doi.org/10.1051/0004-6361/202450522">https://doi.org/10.1051/0004-6361/202450522</a>.
  ieee: J. Matharu <i>et al.</i>, “A first look at spatially resolved star formation
    at 4.8 &#60; z &#60; 6.5 with JWST FRESCO NIRCam slitless spectroscopy,” <i>Astronomy
    and Astrophysics</i>, vol. 690. EDP Sciences, 2024.
  ista: Matharu J, Nelson EJ, Brammer G, Oesch PA, Allen N, Shivaei I, Naidu RP, Chisholm
    J, Covelo-Paz A, Fudamoto Y, Giovinazzo E, Herard-Demanche T, Kerutt J, Kramarenko
    I, Marchesini D, Meyer RA, Prieto-Lyon G, Reddy N, Shuntov M, Weibel A, Wuyts
    S, Xiao M. 2024. A first look at spatially resolved star formation at 4.8 &#60;
    z &#60; 6.5 with JWST FRESCO NIRCam slitless spectroscopy. Astronomy and Astrophysics.
    690, A64.
  mla: Matharu, Jasleen, et al. “A First Look at Spatially Resolved Star Formation
    at 4.8 &#60; z &#60; 6.5 with JWST FRESCO NIRCam Slitless Spectroscopy.” <i>Astronomy
    and Astrophysics</i>, vol. 690, A64, EDP Sciences, 2024, doi:<a href="https://doi.org/10.1051/0004-6361/202450522">10.1051/0004-6361/202450522</a>.
  short: J. Matharu, E.J. Nelson, G. Brammer, P.A. Oesch, N. Allen, I. Shivaei, R.P.
    Naidu, J. Chisholm, A. Covelo-Paz, Y. Fudamoto, E. Giovinazzo, T. Herard-Demanche,
    J. Kerutt, I. Kramarenko, D. Marchesini, R.A. Meyer, G. Prieto-Lyon, N. Reddy,
    M. Shuntov, A. Weibel, S. Wuyts, M. Xiao, Astronomy and Astrophysics 690 (2024).
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-08T14:22:57Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.1051/0004-6361/202450522
external_id:
  arxiv:
  - '2404.17629'
  isi:
  - '001322237700004'
file:
- access_level: open_access
  checksum: 10ae78291aa9fa9a9e64724c42d91588
  content_type: application/pdf
  creator: dernst
  date_created: 2024-10-21T11:45:35Z
  date_updated: 2024-10-21T11:45:35Z
  file_id: '18457'
  file_name: 2024_AstronomyAstrophysics_Matharu.pdf
  file_size: 825494
  relation: main_file
  success: 1
file_date_updated: 2024-10-21T11:45:35Z
has_accepted_license: '1'
intvolume: '       690'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: A first look at spatially resolved star formation at 4.8 < z < 6.5 with JWST
  FRESCO NIRCam slitless spectroscopy
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: 690
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18448'
abstract:
- lang: eng
  text: "Aims. This paper utilises the James Webb Space Telescope (JWST) Mid-Infrared
    Instrument (MIRI) to extend the observational studies of dust and polycyclic aromatic
    hydrocarbon (PAH) emission to a new mass and star formation rate (SFR) parameter
    space beyond our local Universe. The combination of fully sampled spectral energy
    distributions (SEDs) with multiple mid-infrared (mid-IR) bands and the unprecedented
    sensitivity of MIRI allows us to investigate dust obscuration and PAH behaviour
    from z = 0.7 up to z = 2 in typical main-sequence galaxies. Our focus is on constraining
    the evolution of PAH strength and the dust-obscured luminosity fraction before
    and during cosmic noon, the epoch of peak star formation activity in the Universe.\r\n\r\nMethods.
    In this study, we utilise MIRI multi-band imaging data from the SMILES survey
    (5 to 25 μm), complemented with NIRCam photometry from the JADES survey (1 to
    5 μm), available HST photometry (0.4 to 0.9 μm), and spectroscopic redshifts from
    the FRESCO and JADES surveys in GOODS-S for 443 star-forming (without dominant
    active galactic nucleus (AGN)) galaxies at z = 0.7 − 2.0. This redshift range
    was chosen to ensure that the MIRI data cover mid-IR dust emission. Our methodology
    involved employing ultraviolet (UV) to IR energy balance SED fitting to robustly
    constrain the fraction of dust mass in PAHs and dust-obscured luminosity. Additionally,
    we inferred dust sizes from MIRI 15 μm imaging data, enhancing our understanding
    of the physical characteristics of dust within these galaxies.\r\n\r\nResults.
    We find a strong correlation between the fraction of dust in PAHs (PAH fraction,
    qPAH) with stellar mass. Moreover, the sub-sample with robust qPAH measurements
    (N = 216) shows a similar behaviour between qPAH and gas-phase metallicity to
    that at z ∼ 0, suggesting a universal relation: qPAH is constant (∼3.4%) above
    a metallicity of Z ∼ 0.5 Z⊙ and decreases to < 1% at metallicities ≲0.3 Z⊙. This
    indicates that metallicity is a good indicator of the interstellar medium properties
    that affect the balance between the formation and destruction of PAHs. The lack
    of a redshift evolution from z ∼ 0 − 2 also implies that above Z ∼ 0.5 Z⊙ the
    PAH emission effectively traces obscured luminosity and the previous locally calibrated
    PAH-SFR calibrations remain applicable in this metallicity regime. We observe
    a strong correlation between the obscured UV luminosity fraction (ratio of obscured
    to total luminosity) and stellar mass. Above the stellar mass of M* > 5 × 109
    M⊙, on average, more than half of the emitted luminosity is obscured, while there
    exists a non-negligible population of lower-mass galaxies with > 50% obscured
    fractions. At a fixed mass, the obscured fraction correlates with SFR surface
    density. This is a result of higher dust covering fractions in galaxies with more
    compact star-forming regions. Similarly, galaxies with high IRX (IR to UV luminosity)
    at a given mass or UV continuum slope (β) tend to have higher ΣSFR and shallower
    attenuation curves, owing to their higher effective dust optical depths and more
    compact star-forming regions."
acknowledgement: IS thanks the members of the JWST/MIRI instrument team for their
  exceptional efforts and for providing an outstanding experience during the commissioning
  period of JWST, which fostered numerous fruitful discussions and significantly enhanced
  the quality of data reduction in this study. IS also thanks Karin Sandstrom and
  Joel Leja for their insightful discussions during the scientific development of
  this work. Additionally, IS acknowledges the contribution of Andras Gáspar to the
  construction of the F560W PSF utilised in this research. This work was supported
  in part by NASA grant NNX13AD82G. Part of this research has been funded by Atraccíon
  de Talento Grant No. 2022-T1/TIC-20472 of the Comunidad de Madrid, Spain. AJB and
  AC acknowledges funding from the ‘FirstGalaxies’ Advanced Grant from the European
  Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
  program (Grant agreement No. 789056). The work of CCW is supported by NOIRLab, which
  is managed by the Association of Universities for Research in Astronomy (AURA) under
  a cooperative agreement with the National Science Foundation. PGP-G acknowledges
  support from grant PID2022-139567NB-I00 funded by Spanish Ministerio de Ciencia
  e Innovación CIN/AEI/10.13039/501100011033, FEDER Una manera de hacer Europa. SA
  acknowledges support from the JWST Mid-Infrared Instrument (MIRI) Science Team Lead,
  grant 80NSSC18K0555, from NASA Goddard Space Flight Center to the University of
  Arizona. This work is based on observations made with the NASA/ESA/CSA James Webb
  Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes
  at the Space Telescope Science Institute, which is operated by the Association of
  Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for
  JWST. These observations are associated with program PID 1207, 1080, 1081, 1895,
  1220, 1286, 1287, 1963. Based on observations made with the NASA/ESA Hubble Space
  Telescope, and obtained from the Hubble Legacy Archive, which is a collaboration
  between the Space Telescope Science Institute (STScI/NASA), the Space Telescope
  European Coordinating Facility (ST-ECF/ESAC/ESA) and the Canadian Astronomy Data
  Centre (CADC/NRC/CSA).
article_number: A89
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Irene
  full_name: Shivaei, Irene
  last_name: Shivaei
- first_name: Stacey
  full_name: Alberts, Stacey
  last_name: Alberts
- first_name: Michael
  full_name: Florian, Michael
  last_name: Florian
- first_name: George
  full_name: Rieke, George
  last_name: Rieke
- first_name: Stijn
  full_name: Wuyts, Stijn
  last_name: Wuyts
- first_name: Sarah
  full_name: Bodansky, Sarah
  last_name: Bodansky
- first_name: Andrew J.
  full_name: Bunker, Andrew J.
  last_name: Bunker
- first_name: Alex J.
  full_name: Cameron, Alex J.
  last_name: Cameron
- first_name: Mirko
  full_name: Curti, Mirko
  last_name: Curti
- first_name: Francesco
  full_name: Da'Eugenio, Francesco
  last_name: Da'Eugenio
- first_name: Ugne
  full_name: Dudzevičiūte, Ugne
  last_name: Dudzevičiūte
- first_name: Zhiyuan
  full_name: Ji, Zhiyuan
  last_name: Ji
- first_name: Benjamin D.
  full_name: Johnson, Benjamin D.
  last_name: Johnson
- first_name: Ivan
  full_name: Kramarenko, Ivan
  id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4
  last_name: Kramarenko
  orcid: 0000-0001-5346-6048
- first_name: Jianwei
  full_name: Lyu, Jianwei
  last_name: Lyu
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: Jane
  full_name: Morrison, Jane
  last_name: Morrison
- first_name: Rohan
  full_name: Naidu, Rohan
  last_name: Naidu
- first_name: Pablo G.
  full_name: Pérez-González, Pablo G.
  last_name: Pérez-González
- first_name: Naveen
  full_name: Reddy, Naveen
  last_name: Reddy
- first_name: Brant
  full_name: Robertson, Brant
  last_name: Robertson
- first_name: Yang
  full_name: Sun, Yang
  last_name: Sun
- first_name: Sandro
  full_name: Tacchella, Sandro
  last_name: Tacchella
- first_name: Katherine
  full_name: Whitaker, Katherine
  last_name: Whitaker
- first_name: Christina C.
  full_name: Williams, Christina C.
  last_name: Williams
- first_name: Christopher N.A.
  full_name: Willmer, Christopher N.A.
  last_name: Willmer
- first_name: Joris
  full_name: Witstok, Joris
  last_name: Witstok
- first_name: Mengyuan
  full_name: Xiao, Mengyuan
  last_name: Xiao
- first_name: Yongda
  full_name: Zhu, Yongda
  last_name: Zhu
citation:
  ama: Shivaei I, Alberts S, Florian M, et al. A new census of dust and polycyclic
    aromatic hydrocarbons at z = 0.7-2 with JWST MIRI. <i>Astronomy and Astrophysics</i>.
    2024;690. doi:<a href="https://doi.org/10.1051/0004-6361/202449579">10.1051/0004-6361/202449579</a>
  apa: Shivaei, I., Alberts, S., Florian, M., Rieke, G., Wuyts, S., Bodansky, S.,
    … Zhu, Y. (2024). A new census of dust and polycyclic aromatic hydrocarbons at
    z = 0.7-2 with JWST MIRI. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a
    href="https://doi.org/10.1051/0004-6361/202449579">https://doi.org/10.1051/0004-6361/202449579</a>
  chicago: Shivaei, Irene, Stacey Alberts, Michael Florian, George Rieke, Stijn Wuyts,
    Sarah Bodansky, Andrew J. Bunker, et al. “A New Census of Dust and Polycyclic
    Aromatic Hydrocarbons at z = 0.7-2 with JWST MIRI.” <i>Astronomy and Astrophysics</i>.
    EDP Sciences, 2024. <a href="https://doi.org/10.1051/0004-6361/202449579">https://doi.org/10.1051/0004-6361/202449579</a>.
  ieee: I. Shivaei <i>et al.</i>, “A new census of dust and polycyclic aromatic hydrocarbons
    at z = 0.7-2 with JWST MIRI,” <i>Astronomy and Astrophysics</i>, vol. 690. EDP
    Sciences, 2024.
  ista: Shivaei I, Alberts S, Florian M, Rieke G, Wuyts S, Bodansky S, Bunker AJ,
    Cameron AJ, Curti M, Da’Eugenio F, Dudzevičiūte U, Ji Z, Johnson BD, Kramarenko
    I, Lyu J, Matthee JJ, Morrison J, Naidu R, Pérez-González PG, Reddy N, Robertson
    B, Sun Y, Tacchella S, Whitaker K, Williams CC, Willmer CNA, Witstok J, Xiao M,
    Zhu Y. 2024. A new census of dust and polycyclic aromatic hydrocarbons at z =
    0.7-2 with JWST MIRI. Astronomy and Astrophysics. 690, A89.
  mla: Shivaei, Irene, et al. “A New Census of Dust and Polycyclic Aromatic Hydrocarbons
    at z = 0.7-2 with JWST MIRI.” <i>Astronomy and Astrophysics</i>, vol. 690, A89,
    EDP Sciences, 2024, doi:<a href="https://doi.org/10.1051/0004-6361/202449579">10.1051/0004-6361/202449579</a>.
  short: I. Shivaei, S. Alberts, M. Florian, G. Rieke, S. Wuyts, S. Bodansky, A.J.
    Bunker, A.J. Cameron, M. Curti, F. Da’Eugenio, U. Dudzevičiūte, Z. Ji, B.D. Johnson,
    I. Kramarenko, J. Lyu, J.J. Matthee, J. Morrison, R. Naidu, P.G. Pérez-González,
    N. Reddy, B. Robertson, Y. Sun, S. Tacchella, K. Whitaker, C.C. Williams, C.N.A.
    Willmer, J. Witstok, M. Xiao, Y. Zhu, Astronomy and Astrophysics 690 (2024).
date_created: 2024-10-20T22:02:06Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-03-05T11:19:11Z
day: '01'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.1051/0004-6361/202449579
external_id:
  arxiv:
  - '2402.07989'
  isi:
  - '001381135700006'
file:
- access_level: open_access
  checksum: f399be98968b9ca5611c832a9b1eee2b
  content_type: application/pdf
  creator: dernst
  date_created: 2024-10-21T11:52:29Z
  date_updated: 2024-10-21T11:52:29Z
  file_id: '18458'
  file_name: 2024_AstronomyAstrophysics_Shivaei.pdf
  file_size: 10777358
  relation: main_file
  success: 1
file_date_updated: 2024-10-21T11:52:29Z
has_accepted_license: '1'
intvolume: '       690'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new census of dust and polycyclic aromatic hydrocarbons at z = 0.7-2 with
  JWST MIRI
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: 690
year: '2024'
...
---
OA_type: closed access
_id: '18450'
abstract:
- lang: eng
  text: In this work we present the engineering of a portable platform for sensing
    SERS signals in droplets microfluidics. This system comprised not only the read-out
    platform but also a design for the microfluidic devices optimized to enhanced
    the obtained SERS signals.
acknowledgement: The authors acknowledge the financial support of the project HfPT
  – Health from Portugal, with the reference n.° C644937233-00000047, co-funded by
  Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience
  and Recovery Plan, through the NextGenerationEU Fund.
article_processing_charge: No
author:
- first_name: Sergio
  full_name: Quintero, Sergio
  last_name: Quintero
- first_name: Maria
  full_name: Relvas, Maria
  last_name: Relvas
- first_name: Marta
  full_name: Aranda, Marta
  last_name: Aranda
- first_name: Fernando
  full_name: Nodal, Fernando
  id: 8ad43d5a-1ffe-11ee-8b67-8176f59de781
  last_name: Nodal
  orcid: 0009-0006-4119-4376
- first_name: Lorena
  full_name: Dieguez, Lorena
  last_name: Dieguez
- first_name: Sara
  full_name: Abalde-Cela, Sara
  last_name: Abalde-Cela
citation:
  ama: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable
    Raman platform for SERS droplets microfludics. In: <i>2024 International Conference
    on Optical MEMS and Nanophotonics</i>. Institute of Electrical and Electronics
    Engineers; 2024. doi:<a href="https://doi.org/10.1109/OMN61224.2024.10685279">10.1109/OMN61224.2024.10685279</a>'
  apa: 'Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., &#38; Abalde-Cela,
    S. (2024). Portable Raman platform for SERS droplets microfludics. In <i>2024
    International Conference on Optical MEMS and Nanophotonics</i>. San Sebastian,
    Spain: Institute of Electrical and Electronics Engineers. <a href="https://doi.org/10.1109/OMN61224.2024.10685279">https://doi.org/10.1109/OMN61224.2024.10685279</a>'
  chicago: Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez,
    and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.”
    In <i>2024 International Conference on Optical MEMS and Nanophotonics</i>. Institute
    of Electrical and Electronics Engineers, 2024. <a href="https://doi.org/10.1109/OMN61224.2024.10685279">https://doi.org/10.1109/OMN61224.2024.10685279</a>.
  ieee: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela,
    “Portable Raman platform for SERS droplets microfludics,” in <i>2024 International
    Conference on Optical MEMS and Nanophotonics</i>, San Sebastian, Spain, 2024.
  ista: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024.
    Portable Raman platform for SERS droplets microfludics. 2024 International Conference
    on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics.'
  mla: Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.”
    <i>2024 International Conference on Optical MEMS and Nanophotonics</i>, Institute
    of Electrical and Electronics Engineers, 2024, doi:<a href="https://doi.org/10.1109/OMN61224.2024.10685279">10.1109/OMN61224.2024.10685279</a>.
  short: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela,
    in:, 2024 International Conference on Optical MEMS and Nanophotonics, Institute
    of Electrical and Electronics Engineers, 2024.
conference:
  end_date: 2024-08-01
  location: San Sebastian, Spain
  name: 'OMN: Conference on Optical MEMS and Nanophotonics'
  start_date: 2024-07-28
date_created: 2024-10-20T22:02:07Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2025-09-08T14:19:49Z
day: '27'
department:
- _id: GradSch
doi: 10.1109/OMN61224.2024.10685279
external_id:
  isi:
  - '001327768000060'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
publication: 2024 International Conference on Optical MEMS and Nanophotonics
publication_identifier:
  eissn:
  - 2160-5041
  isbn:
  - '9798350384925'
  issn:
  - 2160-5033
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Portable Raman platform for SERS droplets microfludics
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18451'
abstract:
- lang: eng
  text: Inorganic nanoparticles can be assembled into superlattices with unique optical
    and magnetic properties arising from collective behavior. Protein cages can be
    utilized to guide this assembly by encapsulating nanoparticles and promoting their
    assembly into ordered structures. However, creating ordered multi-component structures
    with different protein cage types and sizes remains a challenge. Here, the co-crystallization
    of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized
    by opposing surface charges and unequal diameter is shown. Precise tuning of the
    electrostatic attraction between the cages enabled the preparation of binary crystals
    with dimensions up to several tens of micrometers. Additionally, binary metal
    nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles
    inside the cavities of the protein cages. The resulting structure adopts an AB2FCC
    configuration that also impacts the dipolar coupling between the particles and
    hence the optical properties of the crystals, providing key insight for the future
    preparation of plasmonic and magnetic nanoparticle metamaterials.
acknowledgement: This work has received funding from the European Research Council
  (ERC) under the European Union's Horizon 2020 research and innovation programme
  (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities
  and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy
  Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers
  of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence
  (2022–2029), project number 346110 and 346112.
article_number: '2408416'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yu
  full_name: Zhou, Yu
  last_name: Zhou
- first_name: Ahmed
  full_name: Shaukat, Ahmed
  last_name: Shaukat
- first_name: Jani
  full_name: Seitsonen, Jani
  last_name: Seitsonen
- first_name: Carlo
  full_name: Rigoni, Carlo
  id: c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0
  last_name: Rigoni
- first_name: Jaakko V.I.
  full_name: Timonen, Jaakko V.I.
  last_name: Timonen
- first_name: Mauri A.
  full_name: Kostiainen, Mauri A.
  last_name: Kostiainen
citation:
  ama: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein
    cage directed assembly of binary nanoparticle superlattices. <i>Advanced Science</i>.
    2024;11(45). doi:<a href="https://doi.org/10.1002/advs.202408416">10.1002/advs.202408416</a>
  apa: Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., &#38;
    Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle
    superlattices. <i>Advanced Science</i>. Wiley. <a href="https://doi.org/10.1002/advs.202408416">https://doi.org/10.1002/advs.202408416</a>
  chicago: Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen,
    and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle
    Superlattices.” <i>Advanced Science</i>. Wiley, 2024. <a href="https://doi.org/10.1002/advs.202408416">https://doi.org/10.1002/advs.202408416</a>.
  ieee: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A.
    Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,”
    <i>Advanced Science</i>, vol. 11, no. 45. Wiley, 2024.
  ista: Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024.
    Protein cage directed assembly of binary nanoparticle superlattices. Advanced
    Science. 11(45), 2408416.
  mla: Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.”
    <i>Advanced Science</i>, vol. 11, no. 45, 2408416, Wiley, 2024, doi:<a href="https://doi.org/10.1002/advs.202408416">10.1002/advs.202408416</a>.
  short: Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen,
    Advanced Science 11 (2024).
date_created: 2024-10-20T22:02:07Z
date_published: 2024-12-04T00:00:00Z
date_updated: 2025-09-08T14:20:31Z
day: '04'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1002/advs.202408416
external_id:
  isi:
  - '001330745600001'
  pmid:
  - '39401426'
file:
- access_level: open_access
  checksum: 00451eeb2c9eecf1ff41ad243c793a51
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-13T09:16:25Z
  date_updated: 2025-01-13T09:16:25Z
  file_id: '18834'
  file_name: 2024_AdvancedScience_Zhou.pdf
  file_size: 7040083
  relation: main_file
  success: 1
file_date_updated: 2025-01-13T09:16:25Z
has_accepted_license: '1'
intvolume: '        11'
isi: 1
issue: '45'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Advanced Science
publication_identifier:
  eissn:
  - 2198-3844
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein cage directed assembly of binary nanoparticle superlattices
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: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18452'
abstract:
- lang: eng
  text: 'Diffusion models have recently emerged as powerful tools for the generation
    of new molecular and material structures. The key insight is that the noise in
    these models is related to the response of the atoms to displacement, and the
    denoising step is thus analogous to the geometry relaxation of atomistic systems
    starting from a random structure. Building on this, we present a generative method
    called Response Matching (RM), which leverages the fact that each stable material
    or molecule exists at the minimum of its potential energy surface. Any perturbation
    induces a response in energy and stress, driving the structure back to equilibrium.
    Matching this response is closely related to score matching in diffusion models.
    Another important aspect of state-of-the-art diffusion models is the incorporation
    of physical symmetries such as translation, rotation, and periodicity. RM employs
    a machine learning interatomic potential and random structure search as the denoising
    model, inherently respecting these symmetries and exploiting the locality of atomic
    interactions. RM handles both molecules and bulk materials under the same framework.
    Its efficiency and generalization are demonstrated on three systems: a small organic
    molecular data set, stable crystals from the Materials Project, and one-shot learning
    on a single diamond configuration.'
acknowledgement: B.C. thanks Chris Pickard for enlightening discussions.
article_processing_charge: Yes (in subscription journal)
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. Response matching for generating materials and molecules. <i>Journal
    of Chemical Theory and Computation</i>. 2024;20(20):9259-9266. doi:<a href="https://doi.org/10.1021/acs.jctc.4c00998">10.1021/acs.jctc.4c00998</a>
  apa: Cheng, B. (2024). Response matching for generating materials and molecules.
    <i>Journal of Chemical Theory and Computation</i>. American Chemical Society.
    <a href="https://doi.org/10.1021/acs.jctc.4c00998">https://doi.org/10.1021/acs.jctc.4c00998</a>
  chicago: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.”
    <i>Journal of Chemical Theory and Computation</i>. American Chemical Society,
    2024. <a href="https://doi.org/10.1021/acs.jctc.4c00998">https://doi.org/10.1021/acs.jctc.4c00998</a>.
  ieee: B. Cheng, “Response matching for generating materials and molecules,” <i>Journal
    of Chemical Theory and Computation</i>, vol. 20, no. 20. American Chemical Society,
    pp. 9259–9266, 2024.
  ista: Cheng B. 2024. Response matching for generating materials and molecules. Journal
    of Chemical Theory and Computation. 20(20), 9259–9266.
  mla: Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.”
    <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20, American Chemical
    Society, 2024, pp. 9259–66, doi:<a href="https://doi.org/10.1021/acs.jctc.4c00998">10.1021/acs.jctc.4c00998</a>.
  short: B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.
corr_author: '1'
date_created: 2024-10-20T22:02:07Z
date_published: 2024-10-22T00:00:00Z
date_updated: 2025-09-08T14:21:30Z
day: '22'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1021/acs.jctc.4c00998
external_id:
  arxiv:
  - '2405.09057'
  isi:
  - '001330001500001'
  pmid:
  - '39365029'
file:
- access_level: open_access
  checksum: aca0011bba4846140809b5af583daa9a
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-13T09:11:09Z
  date_updated: 2025-01-13T09:11:09Z
  file_id: '18832'
  file_name: 2024_JCTC_Cheng.pdf
  file_size: 4758251
  relation: main_file
  success: 1
file_date_updated: 2025-01-13T09:11:09Z
has_accepted_license: '1'
intvolume: '        20'
isi: 1
issue: '20'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 9259-9266
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
  eissn:
  - 1549-9626
  issn:
  - 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/BingqingCheng/cace
scopus_import: '1'
status: public
title: Response matching for generating materials and molecules
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18465'
abstract:
- lang: eng
  text: The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN)
    transporters and controls virtually all growth and developmental processes. Canonical
    PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical
    PINs is activated by loop phosphorylation by certain kinases. The structure of
    the PIN transmembrane domains was recently determined, their transport properties
    remained poorly characterized, and the role of the loop in the transport process
    was unclear. Here, we determined the quantitative kinetic parameters of auxin
    transport mediated by Arabidopsis PINs to mathematically model auxin distribution
    in roots and to test these predictions in vivo. Using chimeras between transmembrane
    and loop domains of different PINs, we demonstrate a strong correlation between
    transport parameters and physiological output, indicating that the loop domain
    is not only required to activate PIN-mediated auxin transport, but it has an additional
    role in the transport process by a currently unknown mechanism.
acknowledgement: This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H.
  We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and
  Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished
  results and valuable discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: DP
  full_name: Janacek, DP
  last_name: Janacek
- first_name: M
  full_name: Kolb, M
  last_name: Kolb
- first_name: L
  full_name: Schulz, L
  last_name: Schulz
- first_name: J
  full_name: Mergner, J
  last_name: Mergner
- first_name: B
  full_name: Kuster, B
  last_name: Kuster
- first_name: Matous
  full_name: Glanc, Matous
  id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
  last_name: Glanc
  orcid: 0000-0003-0619-7783
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: K
  full_name: Ten Tusscher, K
  last_name: Ten Tusscher
- first_name: C
  full_name: Schwechheimer, C
  last_name: Schwechheimer
- first_name: UZ
  full_name: Hammes, UZ
  last_name: Hammes
citation:
  ama: Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED
    proteins from Arabidopsis and the role of the loop domain in auxin transport.
    <i>Developmental Cell</i>. 2024;59(14):S1534-5807(24)00569-0. doi:<a href="https://doi.org/10.1016/j.devcel.2024.09.020">10.1016/j.devcel.2024.09.020</a>
  apa: Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes,
    U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis
    and the role of the loop domain in auxin transport. <i>Developmental Cell</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.devcel.2024.09.020">https://doi.org/10.1016/j.devcel.2024.09.020</a>
  chicago: Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří
    Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of
    Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain
    in Auxin Transport.” <i>Developmental Cell</i>. Elsevier, 2024. <a href="https://doi.org/10.1016/j.devcel.2024.09.020">https://doi.org/10.1016/j.devcel.2024.09.020</a>.
  ieee: D. Janacek <i>et al.</i>, “Transport properties of canonical PIN-FORMED proteins
    from Arabidopsis and the role of the loop domain in auxin transport,” <i>Developmental
    Cell</i>, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.
  ista: Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher
    K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED
    proteins from Arabidopsis and the role of the loop domain in auxin transport.
    Developmental Cell. 59(14), S1534-5807(24)00569–0.
  mla: Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins
    from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” <i>Developmental
    Cell</i>, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:<a href="https://doi.org/10.1016/j.devcel.2024.09.020">10.1016/j.devcel.2024.09.020</a>.
  short: D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml,
    K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.
date_created: 2024-10-23T08:41:27Z
date_published: 2024-12-16T00:00:00Z
date_updated: 2025-09-08T14:33:17Z
day: '16'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1016/j.devcel.2024.09.020
external_id:
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  - '001390774300001'
  pmid:
  - '39413780'
file:
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month: '12'
oa: 1
oa_version: Published Version
page: S1534-5807(24)00569-0
pmid: 1
publication: Developmental Cell
publication_identifier:
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  - 1878-1551
  issn:
  - 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
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title: Transport properties of canonical PIN-FORMED proteins from Arabidopsis and
  the role of the loop domain in auxin transport
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type: journal_article
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volume: 59
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18479'
abstract:
- lang: eng
  text: The dominance of beneficial mutations is a key evolutionary parameter affecting
    the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate.
    A leading method to infer it is to compare the relative rates of adaptive substitution
    for X-linked and autosomal genes, which—according to a classic model by Charlesworth
    et al. (1987)—is a simple function of the dominance of new beneficial mutations.
    Recent evidence that rates of adaptive substitution are faster for X-linked genes
    implies, accordingly, that beneficial mutations are usually recessive. However,
    this conclusion is incompatible with leading theories of dominance, which predict
    that beneficial mutations tend to be dominant or overdominant with respect to
    fitness. To address this incompatibility, we use Fisher’s geometric model to predict
    the distribution of fitness effects of new mutations and the relative rates of
    positively selected substitution on the X and autosomes. Previous predictions
    of faster-X theory emerge as a special case of our model in which the phenotypic
    effects of mutations are small relative to the distance to the phenotypic optimum.
    But as mutational effects become large relative to the optimum, we observe an
    elevated tempo of positively selected substitutions on the X relative to the autosomes
    across a broader range of dominance conditions, including those predicted by theories
    of dominance. Our results imply that, contrary to previous models, dominant and
    overdominant beneficial mutations can plausibly generate patterns of faster-X
    adaptation. We discuss resulting implications for genomic studies of adaptation
    and inferences of dominance.
acknowledgement: This work was supported by funds from the Australian Research Council
  and The School of Biological Sciences at Monash University. F.R. was funded by a
  H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous
  reviewers for suggestions that substantially improved the paper and breadth of the
  analysis.
article_number: e2406335121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yasmine
  full_name: Mcdonough, Yasmine
  last_name: Mcdonough
- first_name: Filip
  full_name: Ruzicka, Filip
  id: 347955dd-57b0-11ee-9095-c28bdd368f4b
  last_name: Ruzicka
- first_name: Tim
  full_name: Connallon, Tim
  last_name: Connallon
citation:
  ama: Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with
    the relative rates of adaptive substitution on sex chromosomes and autosomes.
    <i>Proceedings of the National Academy of Sciences of the United States of America</i>.
    2024;121(44). doi:<a href="https://doi.org/10.1073/pnas.2406335121">10.1073/pnas.2406335121</a>
  apa: Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories
    of dominance with the relative rates of adaptive substitution on sex chromosomes
    and autosomes. <i>Proceedings of the National Academy of Sciences of the United
    States of America</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.2406335121">https://doi.org/10.1073/pnas.2406335121</a>
  chicago: Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories
    of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes
    and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United
    States of America</i>. National Academy of Sciences, 2024. <a href="https://doi.org/10.1073/pnas.2406335121">https://doi.org/10.1073/pnas.2406335121</a>.
  ieee: Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance
    with the relative rates of adaptive substitution on sex chromosomes and autosomes,”
    <i>Proceedings of the National Academy of Sciences of the United States of America</i>,
    vol. 121, no. 44. National Academy of Sciences, 2024.
  ista: Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance
    with the relative rates of adaptive substitution on sex chromosomes and autosomes.
    Proceedings of the National Academy of Sciences of the United States of America.
    121(44), e2406335121.
  mla: Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative
    Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings
    of the National Academy of Sciences of the United States of America</i>, vol.
    121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href="https://doi.org/10.1073/pnas.2406335121">10.1073/pnas.2406335121</a>.
  short: Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy
    of Sciences of the United States of America 121 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2025-09-08T14:31:58Z
day: '29'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1073/pnas.2406335121
ec_funded: 1
external_id:
  isi:
  - '001359216400017'
  pmid:
  - '39436652'
file:
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month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the National Academy of Sciences of the United States
  of America
publication_identifier:
  eissn:
  - 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconciling theories of dominance with the relative rates of adaptive substitution
  on sex chromosomes and autosomes
tmp:
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    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18480'
abstract:
- lang: eng
  text: Caloric restriction (CR) can extend the organism life- and health-span by
    improving glucose homeostasis. How CR affects the structure-function of pancreatic
    beta cells remains unknown. We used single nucleus transcriptomics to show that
    CR increases the expression of genes for beta cell identity, protein processing,
    and organelle homeostasis. Gene regulatory network analysis reveal that CR activates
    transcription factors important for beta cell identity and homeostasis, while
    imaging metabolomics demonstrates that beta cells upon CR are more energetically
    competent. In fact, high-resolution microscopy show that CR reduces beta cell
    mitophagy to increase mitochondria mass and the potential for ATP generation.
    However, CR beta cells have impaired adaptive proliferation in response to high
    fat diet feeding. Finally, we show that long-term CR delays the onset of beta
    cell aging hallmarks and promotes cell longevity by reducing beta cell turnover.
    Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function
    during aging and diabetes.
acknowledgement: We are thankful to Michelle Reyzer from the Vanderbilt Mass Spectrometry
  Research Center for assistance with MALDI-MS imaging and analysis, to the outstanding
  team at the Vanderbilt Mouse Metabolic Phenotyping Center for all the assistance
  with in vivo glucose homeostasis tests (DK135073, 1S10RR028101-01). We also thank
  the University of Michigan Animal Phenotyping Core for conducting the bomb calorimetry
  experiments (1U2CDK110768, DK020575, and DK089503). This research was supported
  by recruitment funds from the Vanderbilt’s Department of Molecular Physiology and
  Biophysics and NIH grants 1R03DK127484, 5U24DK097771, and 1R01DK138141 to RAeD,
  by a grant from the Canadian Institutes of Health Research (CIHR; 487188) to PEM,
  by and NIH DK132669 to D.D. PEM holds the Canada Research Chair in Islet Biology.
article_number: '9063'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cristiane
  full_name: Dos Santos, Cristiane
  last_name: Dos Santos
- first_name: Amanda
  full_name: Cambraia, Amanda
  last_name: Cambraia
- first_name: Shristi
  full_name: Shrestha, Shristi
  last_name: Shrestha
- first_name: Melanie
  full_name: Cutler, Melanie
  last_name: Cutler
- first_name: Matthew
  full_name: Cottam, Matthew
  last_name: Cottam
- first_name: Guy
  full_name: Perkins, Guy
  last_name: Perkins
- first_name: Varda
  full_name: Lev-Ram, Varda
  last_name: Lev-Ram
- first_name: Birbickram
  full_name: Roy, Birbickram
  last_name: Roy
- first_name: Christopher
  full_name: Acree, Christopher
  last_name: Acree
- first_name: Keun Young
  full_name: Kim, Keun Young
  last_name: Kim
- first_name: Thomas
  full_name: Deerinck, Thomas
  last_name: Deerinck
- first_name: Danielle
  full_name: Dean, Danielle
  last_name: Dean
- first_name: Jean Philippe
  full_name: Cartailler, Jean Philippe
  last_name: Cartailler
- first_name: Patrick E.
  full_name: Macdonald, Patrick E.
  last_name: Macdonald
- first_name: Martin W
  full_name: Hetzer, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: Hetzer
  orcid: 0000-0002-2111-992X
- first_name: Mark
  full_name: Ellisman, Mark
  last_name: Ellisman
- first_name: Rafael
  full_name: Arrojo E Drigo, Rafael
  last_name: Arrojo E Drigo
citation:
  ama: Dos Santos C, Cambraia A, Shrestha S, et al. Calorie restriction increases
    insulin sensitivity to promote beta cell homeostasis and longevity in mice. <i>Nature
    Communications</i>. 2024;15. doi:<a href="https://doi.org/10.1038/s41467-024-53127-2">10.1038/s41467-024-53127-2</a>
  apa: Dos Santos, C., Cambraia, A., Shrestha, S., Cutler, M., Cottam, M., Perkins,
    G., … Arrojo E Drigo, R. (2024). Calorie restriction increases insulin sensitivity
    to promote beta cell homeostasis and longevity in mice. <i>Nature Communications</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41467-024-53127-2">https://doi.org/10.1038/s41467-024-53127-2</a>
  chicago: Dos Santos, Cristiane, Amanda Cambraia, Shristi Shrestha, Melanie Cutler,
    Matthew Cottam, Guy Perkins, Varda Lev-Ram, et al. “Calorie Restriction Increases
    Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature
    Communications</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s41467-024-53127-2">https://doi.org/10.1038/s41467-024-53127-2</a>.
  ieee: C. Dos Santos <i>et al.</i>, “Calorie restriction increases insulin sensitivity
    to promote beta cell homeostasis and longevity in mice,” <i>Nature Communications</i>,
    vol. 15. Springer Nature, 2024.
  ista: Dos Santos C, Cambraia A, Shrestha S, Cutler M, Cottam M, Perkins G, Lev-Ram
    V, Roy B, Acree C, Kim KY, Deerinck T, Dean D, Cartailler JP, Macdonald PE, Hetzer
    M, Ellisman M, Arrojo E Drigo R. 2024. Calorie restriction increases insulin sensitivity
    to promote beta cell homeostasis and longevity in mice. Nature Communications.
    15, 9063.
  mla: Dos Santos, Cristiane, et al. “Calorie Restriction Increases Insulin Sensitivity
    to Promote Beta Cell Homeostasis and Longevity in Mice.” <i>Nature Communications</i>,
    vol. 15, 9063, Springer Nature, 2024, doi:<a href="https://doi.org/10.1038/s41467-024-53127-2">10.1038/s41467-024-53127-2</a>.
  short: C. Dos Santos, A. Cambraia, S. Shrestha, M. Cutler, M. Cottam, G. Perkins,
    V. Lev-Ram, B. Roy, C. Acree, K.Y. Kim, T. Deerinck, D. Dean, J.P. Cartailler,
    P.E. Macdonald, M. Hetzer, M. Ellisman, R. Arrojo E Drigo, Nature Communications
    15 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-21T00:00:00Z
date_updated: 2025-09-08T14:32:38Z
day: '21'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1038/s41467-024-53127-2
external_id:
  isi:
  - '001426270600023'
  pmid:
  - '39433757'
file:
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  creator: dernst
  date_created: 2024-11-04T10:37:56Z
  date_updated: 2024-11-04T10:37:56Z
  file_id: '18502'
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  success: 1
file_date_updated: 2024-11-04T10:37:56Z
has_accepted_license: '1'
intvolume: '        15'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Calorie restriction increases insulin sensitivity to promote beta cell homeostasis
  and longevity in mice
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: 15
year: '2024'
...
---
OA_type: closed access
_id: '18482'
abstract:
- lang: eng
  text: "This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact
    convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a
    shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case
    of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev
    center and the Chebyshev radius of A. This paper focuses on the case in which
    A and B are defined with their black-box support functions. An algorithm for solving
    such problems efficiently is suggested. The algorithm has a superlinear convergence
    rate, and it can solve hundred-dimensional test problems in a reasonable time,
    but some additional conditions on A and B are required to guarantee the presence
    of convergence. Additionally, the behavior of the algorithm for a simple special
    case is investigated, which leads to a number of theoretical results. Perturbations
    of this special case are also studied."
acknowledgement: The author is grateful to Maxim Balashov for setting the problem,
  providing useful literature, important discussions and text review. Also, I thank
  Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support.
article_processing_charge: No
article_type: original
author:
- first_name: Pavel
  full_name: Arkhipov, Pavel
  id: b25f2ab2-1fed-11ee-8599-fe02d211784f
  last_name: Arkhipov
citation:
  ama: Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets
    defined via their support functions. <i>Automation and Remote Control</i>. 2024;85(6):522-532.
    doi:<a href="https://doi.org/10.1134/S0005117924060031">10.1134/S0005117924060031</a>
  apa: Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center
    of sets defined via their support functions. <i>Automation and Remote Control</i>.
    Springer Nature. <a href="https://doi.org/10.1134/S0005117924060031">https://doi.org/10.1134/S0005117924060031</a>
  chicago: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center
    of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>.
    Springer Nature, 2024. <a href="https://doi.org/10.1134/S0005117924060031">https://doi.org/10.1134/S0005117924060031</a>.
  ieee: P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of
    sets defined via their support functions,” <i>Automation and Remote Control</i>,
    vol. 85, no. 6. Springer Nature, pp. 522–532, 2024.
  ista: Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center
    of sets defined via their support functions. Automation and Remote Control. 85(6),
    522–532.
  mla: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center
    of Sets Defined via Their Support Functions.” <i>Automation and Remote Control</i>,
    vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:<a href="https://doi.org/10.1134/S0005117924060031">10.1134/S0005117924060031</a>.
  short: P. Arkhipov, Automation and Remote Control 85 (2024) 522–532.
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2025-09-08T14:27:08Z
day: '01'
department:
- _id: GradSch
doi: 10.1134/S0005117924060031
external_id:
  isi:
  - '001338721700007'
intvolume: '        85'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 522-532
publication: Automation and Remote Control
publication_identifier:
  eissn:
  - 1608-3032
  issn:
  - 0005-1179
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An algorithm for finding the generalized Chebyshev center of sets defined via
  their support functions
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 85
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18483'
abstract:
- lang: eng
  text: In this paper we prove a perturbative version of a remarkable Bialy–Mironov
    (Ann. Math. 196(1):389–413, 2022) result. They prove non perturbative Birkhoff
    conjecture for centrally-symmetric convex domains, namely, a centrally-symmetric
    convex domain with integrable billiard is ellipse. We combine techniques from
    Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) with a local result by Kaloshin–Sorrentino
    (Ann. Math. 188(1):315–380, 2018) and show that a domain close enough to a centrally
    symmetric one with integrable billiard is ellipse. To combine these results we
    derive a slight extension of Bialy–Mironov (Ann. Math. 196(1):389–413, 2022) by
    proving that a notion of rational integrability is equivalent to the C0-integrability
    condition used in their paper.
acknowledgement: We are grateful to the anonymous referee for their careful reading
  and valuable remarks and comments which helped to improve significantly the paper.
  Open access funding provided by Institute of Science and Technology (IST Austria).
  V.K. and C.E.K. gratefully acknowledge support from the European Research Council
  (ERC) through the Advanced Grant “SPERIG” (#885 707).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Vadim
  full_name: Kaloshin, Vadim
  id: FE553552-CDE8-11E9-B324-C0EBE5697425
  last_name: Kaloshin
  orcid: 0000-0002-6051-2628
- first_name: Edmond
  full_name: Koudjinan, Edmond
  id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
  last_name: Koudjinan
  orcid: 0000-0003-2640-4049
- first_name: Ke
  full_name: Zhang, Ke
  last_name: Zhang
citation:
  ama: Kaloshin V, Koudjinan E, Zhang K. Birkhoff conjecture for nearly centrally
    symmetric domains. <i>Geometric and Functional Analysis</i>. 2024;34:1973-2007.
    doi:<a href="https://doi.org/10.1007/s00039-024-00695-6">10.1007/s00039-024-00695-6</a>
  apa: Kaloshin, V., Koudjinan, E., &#38; Zhang, K. (2024). Birkhoff conjecture for
    nearly centrally symmetric domains. <i>Geometric and Functional Analysis</i>.
    Springer Nature. <a href="https://doi.org/10.1007/s00039-024-00695-6">https://doi.org/10.1007/s00039-024-00695-6</a>
  chicago: Kaloshin, Vadim, Edmond Koudjinan, and Ke Zhang. “Birkhoff Conjecture for
    Nearly Centrally Symmetric Domains.” <i>Geometric and Functional Analysis</i>.
    Springer Nature, 2024. <a href="https://doi.org/10.1007/s00039-024-00695-6">https://doi.org/10.1007/s00039-024-00695-6</a>.
  ieee: V. Kaloshin, E. Koudjinan, and K. Zhang, “Birkhoff conjecture for nearly centrally
    symmetric domains,” <i>Geometric and Functional Analysis</i>, vol. 34. Springer
    Nature, pp. 1973–2007, 2024.
  ista: Kaloshin V, Koudjinan E, Zhang K. 2024. Birkhoff conjecture for nearly centrally
    symmetric domains. Geometric and Functional Analysis. 34, 1973–2007.
  mla: Kaloshin, Vadim, et al. “Birkhoff Conjecture for Nearly Centrally Symmetric
    Domains.” <i>Geometric and Functional Analysis</i>, vol. 34, Springer Nature,
    2024, pp. 1973–2007, doi:<a href="https://doi.org/10.1007/s00039-024-00695-6">10.1007/s00039-024-00695-6</a>.
  short: V. Kaloshin, E. Koudjinan, K. Zhang, Geometric and Functional Analysis 34
    (2024) 1973–2007.
corr_author: '1'
date_created: 2024-10-27T23:01:45Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-08T14:27:45Z
day: '01'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1007/s00039-024-00695-6
ec_funded: 1
external_id:
  arxiv:
  - '2306.12301'
  isi:
  - '001329804200001'
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has_accepted_license: '1'
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language:
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month: '12'
oa: 1
oa_version: Published Version
page: 1973-2007
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
  call_identifier: H2020
  grant_number: '885707'
  name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Geometric and Functional Analysis
publication_identifier:
  eissn:
  - 1420-8970
  issn:
  - 1016-443X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Birkhoff conjecture for nearly centrally symmetric domains
tmp:
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  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
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---
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abstract:
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  text: The advancement of quantum simulators motivates the development of a theoretical
    framework to assist with efficient state preparation in quantum many-body systems.
    Generally, preparing a target entangled state via unitary evolution with time-dependent
    couplings is a challenging task and very little is known about the existence of
    solutions and their properties. In this work we develop a constructive approach
    for preparing matrix product states (MPS) via continuous unitary evolution. We
    provide an explicit construction of the operator that exactly implements the evolution
    of a given MPS along a specified direction in its tangent space. This operator
    can be written as a sum of local terms of finite range, yet it is in general non-Hermitian.
    Relying on the explicit construction of the non-Hermitian generator of the dynamics,
    we demonstrate the existence of a Hermitian sequence of operators that implements
    the desired MPS evolution with an error that decreases exponentially with the
    operator range. The construction is benchmarked on an explicit periodic trajectory
    in a translationally invariant MPS manifold. We demonstrate that the Floquet unitary
    generating the dynamics over one period of the trajectory features an approximate
    MPS-like eigenstate embedded among a sea of thermalizing eigenstates. These results
    show that our construction is not only useful for state preparation and control
    of many-body systems, but also provides a generic route towards Floquet scars—periodically
    driven models with quasilocal generators of dynamics that have exact MPS eigenstates
    in their spectrum.
acknowledgement: We thank L. Piroli, S. Garratt, and A. Molnár for insightful discussions.
  This research was funded in part by the European Research Council (ERC) under the
  European Union’s Horizon 2020 research and innovation programme (Grant Agreements
  No. 850899 and No. 863476), the Austrian Science Fund (FWF) (Grant DOIs 10.55776/COE1,
  10.55776/P36305, and 10.55776/F71), and the European Union (NextGenerationEU). This
  work was performed in part at the Aspen Center for Physics, which is supported by
  National Science Foundation Grant PHY-2210452. This research was supported in part
  by NSF Grant PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).
article_number: '040311'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Marko
  full_name: Ljubotina, Marko
  id: F75EE9BE-5C90-11EA-905D-16643DDC885E
  last_name: Ljubotina
  orcid: 0000-0003-0038-7068
- first_name: Elena
  full_name: Petrova, Elena
  id: 0ac84990-897b-11ed-a09c-f5abb56a4ede
  last_name: Petrova
- first_name: Norbert
  full_name: Schuch, Norbert
  last_name: Schuch
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
citation:
  ama: Ljubotina M, Petrova E, Schuch N, Serbyn M. Tangent space generators of matrix
    product states and exact floquet quantum scars. <i>PRX Quantum</i>. 2024;5(4).
    doi:<a href="https://doi.org/10.1103/prxquantum.5.040311">10.1103/prxquantum.5.040311</a>
  apa: Ljubotina, M., Petrova, E., Schuch, N., &#38; Serbyn, M. (2024). Tangent space
    generators of matrix product states and exact floquet quantum scars. <i>PRX Quantum</i>.
    American Physical Society. <a href="https://doi.org/10.1103/prxquantum.5.040311">https://doi.org/10.1103/prxquantum.5.040311</a>
  chicago: Ljubotina, Marko, Elena Petrova, Norbert Schuch, and Maksym Serbyn. “Tangent
    Space Generators of Matrix Product States and Exact Floquet Quantum Scars.” <i>PRX
    Quantum</i>. American Physical Society, 2024. <a href="https://doi.org/10.1103/prxquantum.5.040311">https://doi.org/10.1103/prxquantum.5.040311</a>.
  ieee: M. Ljubotina, E. Petrova, N. Schuch, and M. Serbyn, “Tangent space generators
    of matrix product states and exact floquet quantum scars,” <i>PRX Quantum</i>,
    vol. 5, no. 4. American Physical Society, 2024.
  ista: Ljubotina M, Petrova E, Schuch N, Serbyn M. 2024. Tangent space generators
    of matrix product states and exact floquet quantum scars. PRX Quantum. 5(4), 040311.
  mla: Ljubotina, Marko, et al. “Tangent Space Generators of Matrix Product States
    and Exact Floquet Quantum Scars.” <i>PRX Quantum</i>, vol. 5, no. 4, 040311, American
    Physical Society, 2024, doi:<a href="https://doi.org/10.1103/prxquantum.5.040311">10.1103/prxquantum.5.040311</a>.
  short: M. Ljubotina, E. Petrova, N. Schuch, M. Serbyn, PRX Quantum 5 (2024).
corr_author: '1'
date_created: 2024-10-29T16:04:05Z
date_published: 2024-10-23T00:00:00Z
date_updated: 2025-09-08T14:26:29Z
day: '23'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1103/prxquantum.5.040311
ec_funded: 1
external_id:
  arxiv:
  - '2403.12325'
  isi:
  - '001346198800001'
file:
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  creator: dernst
  date_created: 2024-10-30T08:59:09Z
  date_updated: 2024-10-30T08:59:09Z
  file_id: '18489'
  file_name: 2024_PRXQuantum_Ljubotina.pdf
  file_size: 1151431
  relation: main_file
  success: 1
file_date_updated: 2024-10-30T08:59:09Z
has_accepted_license: '1'
intvolume: '         5'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
  call_identifier: H2020
  grant_number: '850899'
  name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: PRX Quantum
publication_identifier:
  eissn:
  - 2691-3399
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tangent space generators of matrix product states and exact floquet quantum
  scars
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: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18490'
abstract:
- lang: eng
  text: 'For large classes of even-dimensional Riemannian manifolds (Formula presented.),
    we construct and analyze conformally invariant random fields. These centered Gaussian
    fields (Formula presented.), called co-polyharmonic Gaussian fields, are characterized
    by their covariance kernels k which exhibit a precise logarithmic divergence:
    (Formula presented.). They share a fundamental quasi-invariance property under
    conformal transformations. In terms of the co-polyharmonic Gaussian field (Formula
    presented.), we define the Liouville Quantum Gravity measure, a random measure
    on (Formula presented.), heuristically given as (Formula presented.) and rigorously
    obtained as almost sure weak limit of the right-hand side with (Formula presented.)
    replaced by suitable regular approximations (Formula presented.). In terms on
    the Liouville Quantum Gravity measure, we define the Liouville Brownian motion
    on (Formula presented.) and the random GJMS operators. Finally, we present an
    approach to a conformal field theory in arbitrary even dimension with an ansatz
    based on Branson''s (Formula presented.) -curvature: we give a rigorous meaning
    to the Polyakov–Liouville measure (Formula presented.) and we derive the corresponding
    conformal anomaly. The set of admissible manifolds is conformally invariant. It
    includes all compact 2-dimensional Riemannian manifolds, all compact non-negatively
    curved Einstein manifolds of even dimension, and large classes of compact hyperbolic
    manifolds of even dimension. However, not every compact even-dimensional Riemannian
    manifold is admissible. Our results concerning the logarithmic divergence of the
    kernel (Formula presented.) rely on new sharp estimates for heat kernels and higher
    order Green kernels on arbitrary closed manifolds. '
acknowledgement: The authors are grateful to Masha Gordina for helpful references,
  and to Nathanaël Berestycki, Baptiste Cerclé, and Ewain Gwynne for valuable comments
  on the first circulated version of this paper. They also would like to thank Sebastian
  Andres, Peter Friz, and Yizheng Yuan for pointing out an erroneous formulation in
  the previous version of Theorem 5.7. Moreover, KTS would liketo express his thanks
  to Sebastian Andres, Matthias Erbar, Martin Huesmann, and Jan Mass for stimulating
  discussions on previous attempts to this project. LDS gratefully acknowledges financial
  support from the European Research Council (grant agreement No 716117, awarded to
  J. Maas), from the Austrian Science Fund (FWF) project 10.55776/ESP208, and from
  the Austrian Science Fund (FWF) project 10.55776/F65.RH, EK, and KTS gratefully
  acknowledge funding by the Deutsche Forschungsgemeinschaft through the project “Random
  Riemannian Geometry” within the SPP 2265 “Random Geomet-ric Systems,” through the
  Hausdorff Center for Mathematics (project ID 390685813), and through project B03
  within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledge
  financial support from the European Research Council through the ERC AdG “RicciBounds”(grant
  agreement 694405).Data sharing not applicable to this article as no datasets were
  generated or analyzed during the current study. Open access funding enabled and
  organized by Projekt DEAL.
article_number: e70003
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lorenzo
  full_name: Dello Schiavo, Lorenzo
  id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
  last_name: Dello Schiavo
  orcid: 0000-0002-9881-6870
- first_name: Ronan
  full_name: Herry, Ronan
  last_name: Herry
- first_name: Eva
  full_name: Kopfer, Eva
  last_name: Kopfer
- first_name: Karl Theodor
  full_name: Sturm, Karl Theodor
  last_name: Sturm
citation:
  ama: Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Conformally invariant random
    fields, Liouville quantum gravity measures, and random Paneitz operators on Riemannian
    manifolds of even dimension. <i>Journal of the London Mathematical Society</i>.
    2024;110(5). doi:<a href="https://doi.org/10.1112/jlms.70003">10.1112/jlms.70003</a>
  apa: Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2024). Conformally
    invariant random fields, Liouville quantum gravity measures, and random Paneitz
    operators on Riemannian manifolds of even dimension. <i>Journal of the London
    Mathematical Society</i>. London Mathematical Society. <a href="https://doi.org/10.1112/jlms.70003">https://doi.org/10.1112/jlms.70003</a>
  chicago: Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm.
    “Conformally Invariant Random Fields, Liouville Quantum Gravity Measures, and
    Random Paneitz Operators on Riemannian Manifolds of Even Dimension.” <i>Journal
    of the London Mathematical Society</i>. London Mathematical Society, 2024. <a
    href="https://doi.org/10.1112/jlms.70003">https://doi.org/10.1112/jlms.70003</a>.
  ieee: L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Conformally invariant
    random fields, Liouville quantum gravity measures, and random Paneitz operators
    on Riemannian manifolds of even dimension,” <i>Journal of the London Mathematical
    Society</i>, vol. 110, no. 5. London Mathematical Society, 2024.
  ista: Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2024. Conformally invariant
    random fields, Liouville quantum gravity measures, and random Paneitz operators
    on Riemannian manifolds of even dimension. Journal of the London Mathematical
    Society. 110(5), e70003.
  mla: Dello Schiavo, Lorenzo, et al. “Conformally Invariant Random Fields, Liouville
    Quantum Gravity Measures, and Random Paneitz Operators on Riemannian Manifolds
    of Even Dimension.” <i>Journal of the London Mathematical Society</i>, vol. 110,
    no. 5, e70003, London Mathematical Society, 2024, doi:<a href="https://doi.org/10.1112/jlms.70003">10.1112/jlms.70003</a>.
  short: L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Journal of the London
    Mathematical Society 110 (2024).
date_created: 2024-11-03T23:01:44Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-08T14:29:45Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1112/jlms.70003
ec_funded: 1
external_id:
  isi:
  - '001351918100029'
file:
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  checksum: 143816823b5f43bd3748da8e3e91cef5
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  creator: dernst
  date_created: 2024-11-04T08:54:26Z
  date_updated: 2024-11-04T08:54:26Z
  file_id: '18497'
  file_name: 2024_JourLondonMathSoc_Schiavo.pdf
  file_size: 911476
  relation: main_file
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file_date_updated: 2024-11-04T08:54:26Z
has_accepted_license: '1'
intvolume: '       110'
isi: 1
issue: '5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '716117'
  name: Optimal Transport and Stochastic Dynamics
- _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c
  grant_number: E208
  name: Configuration Spaces over Non-Smooth Spaces
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
  grant_number: F6504
  name: Taming Complexity in Partial Differential Systems
publication: Journal of the London Mathematical Society
publication_identifier:
  eissn:
  - 1469-7750
  issn:
  - 0024-6107
publication_status: published
publisher: London Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Conformally invariant random fields, Liouville quantum gravity measures, and
  random Paneitz operators on Riemannian manifolds of even dimension
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2024'
...
