---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19421'
abstract:
- lang: eng
  text: The phytohormone auxin (Aux) is a principal endogenous developmental signal
    in plants. It mediates transcriptional reprogramming by a well-established canonical
    signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin
    ligase complex; after auxin perception, they associate with Aux/IAA transcriptional
    repressors and ubiquitinate them for degradation, thus enabling the activation
    of auxin response factor (ARF) transcription factors1,2,3. Here we revise this
    paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced
    degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin
    response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation
    of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming
    and auxin-regulated development, including shoot, root, root hair growth and lateral
    root formation. Transgenic plants show that local cAMP production in the vicinity
    of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin
    perception and is sufficient to induce ARF-mediated transcription. These discoveries
    revise the canonical model of auxin signalling and establish TIR1/AFB-produced
    cAMP as a second messenger essential for transcriptional reprograming.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: We are grateful to J. Callis and H.-Q. Yang for sharing materials
  and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported
  by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics
  Facility of the Institute of Science and Technology Austria. This project has received
  funding from the European Research Council (101142681 CYNIPS) and Austrian Science
  Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation
  of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project
  Committee of the Institute of Science and Technology Austria, and Y.P. was supported
  by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided
  by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Huihuang
  full_name: Chen, Huihuang
  id: 83c96512-15b2-11ec-abd3-b7eede36184f
  last_name: Chen
- first_name: Linlin
  full_name: Qi, Linlin
  id: 44B04502-A9ED-11E9-B6FC-583AE6697425
  last_name: Qi
  orcid: 0000-0001-5187-8401
- first_name: Minxia
  full_name: Zou, Minxia
  id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
  last_name: Zou
- first_name: Mengting
  full_name: Lu, Mengting
  id: a8198a14-1ffe-11ee-8b67-d2bdff9d9178
  last_name: Lu
- first_name: M
  full_name: Kwiatkowski, M
  last_name: Kwiatkowski
- first_name: Yuanrong
  full_name: Pei, Yuanrong
  id: 98605edc-6ce7-11ee-95f3-cc16b866efcd
  last_name: Pei
- first_name: K
  full_name: Jaworski, K
  last_name: Jaworski
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Chen H, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional
    auxin signalling. <i>Nature</i>. 2025;640:1011-1016. doi:<a href="https://doi.org/10.1038/s41586-025-08669-w">10.1038/s41586-025-08669-w</a>
  apa: Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025).
    TIR1-produced cAMP as a second messenger in transcriptional auxin signalling.
    <i>Nature</i>. Springer Nature. <a href="https://doi.org/10.1038/s41586-025-08669-w">https://doi.org/10.1038/s41586-025-08669-w</a>
  chicago: Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong
    Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in
    Transcriptional Auxin Signalling.” <i>Nature</i>. Springer Nature, 2025. <a href="https://doi.org/10.1038/s41586-025-08669-w">https://doi.org/10.1038/s41586-025-08669-w</a>.
  ieee: H. Chen <i>et al.</i>, “TIR1-produced cAMP as a second messenger in transcriptional
    auxin signalling,” <i>Nature</i>, vol. 640. Springer Nature, pp. 1011–1016, 2025.
  ista: Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025.
    TIR1-produced cAMP as a second messenger in transcriptional auxin signalling.
    Nature. 640, 1011–1016.
  mla: Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional
    Auxin Signalling.” <i>Nature</i>, vol. 640, Springer Nature, 2025, pp. 1011–16,
    doi:<a href="https://doi.org/10.1038/s41586-025-08669-w">10.1038/s41586-025-08669-w</a>.
  short: H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml,
    Nature 640 (2025) 1011–1016.
corr_author: '1'
date_created: 2025-03-19T09:44:39Z
date_published: 2025-04-24T00:00:00Z
date_updated: 2026-11-14T23:31:17Z
day: '24'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41586-025-08669-w
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  grant_number: P37051
  name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
publication: Nature
publication_identifier:
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  issn:
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publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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status: public
title: TIR1-produced cAMP as a second messenger in transcriptional auxin signalling
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 640
year: '2025'
...
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abstract:
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  text: "Well-defined powder precursors are important for the rational design of crystalline
    inorganic \r\nmaterials with controlled defects and functional properties. Such
    powders can be prepared from \r\ndried nanoparticles synthesized using a surfactant-assisted/colloidal
    method that provides \r\nprecise control over size, shape, composition, and surface
    chemistry of nanoparticles. These \r\ntailored nanoparticles further act as building
    blocks for three-dimensional assemblies, \r\nexhibiting collective nanoscale properties
    and enabling tailored microstructures of crystalline \r\ninorganic materials.
    However, the programmable engineering of such materials using \r\nnanoparticle-based
    precursors remains limited, due to a lack of fundamental understanding of \r\nboth
    the synthesis of nanoparticles and their conversion into macroscopic solids. Furthermore,
    \r\nthe formation of three-dimensional assemblies often requires multi-step post-synthetic
    \r\ntreatments, which can limit reproducibility and the production of the bulk
    inorganic materials. \r\nIn this thesis, I demonstrate a key synthetic parameter
    governing the formation of desired \r\nnanostructures, especially metal/semiconductor
    core–shell nanoparticles which are potential \r\nprecursors for engineering composition,
    crystal structure, and defects of final materials. Then, \r\nI investigate their
    transformative pathways to unveil structural and chemical changes that occur \r\nduring
    heat treatment of the nanoparticle-based precursors. Building on understanding
    of \r\natomic-scale interactions during nanoparticle-based precursor formation,
    I further demonstrate \r\nthe possibility of synthesizing the nanoparticle assembly
    directly in the nanoparticle synthesis \r\nreaction and rationalize the process
    of in situ self-assembly of nanoparticles. Finally, the impact \r\nof NP-based
    precursors on the formation and properties of crystalline inorganic materials
    is \r\nevaluated, demonstrating the potential of employing NP-based precursors
    for the rational \r\ndesign of functional inorganic materials. "
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Seungho
  full_name: Lee, Seungho
  id: BB243B88-D767-11E9-B658-BC13E6697425
  last_name: Lee
  orcid: 0000-0002-6962-8598
citation:
  ama: Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic
    solids. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20415">10.15479/AT-ISTA-20415</a>
  apa: Lee, S. (2025). <i>Nanoparticle-based precursors toward advanced crystalline
    inorganic solids</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-20415">https://doi.org/10.15479/AT-ISTA-20415</a>
  chicago: Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline
    Inorganic Solids.” Institute of Science and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT-ISTA-20415">https://doi.org/10.15479/AT-ISTA-20415</a>.
  ieee: S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic
    solids,” Institute of Science and Technology Austria, 2025.
  ista: Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic
    solids. Institute of Science and Technology Austria.
  mla: Lee, Seungho. <i>Nanoparticle-Based Precursors toward Advanced Crystalline
    Inorganic Solids</i>. Institute of Science and Technology Austria, 2025, doi:<a
    href="https://doi.org/10.15479/AT-ISTA-20415">10.15479/AT-ISTA-20415</a>.
  short: S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic
    Solids, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-01T09:04:00Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-10-23T08:16:15Z
day: '01'
ddc:
- '540'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaIb
doi: 10.15479/AT-ISTA-20415
doi_confirm: '1'
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- iso: eng
month: '10'
oa: 1
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page: '144'
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
  name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
    Semiconductors for Waste Heat Recovery'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '12237'
    relation: part_of_dissertation
    status: public
  - id: '15357'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Maria
  full_name: Ibáñez, Maria
  id: 43C61214-F248-11E8-B48F-1D18A9856A87
  last_name: Ibáñez
  orcid: 0000-0001-5013-2843
- first_name: Loredana
  full_name: Protesescu, Loredana
  last_name: Protesescu
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
title: Nanoparticle-based precursors toward advanced crystalline inorganic solids
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '19763'
abstract:
- lang: eng
  text: "Pattern formation in developing organs is controlled by morphogens. These
    signalling\r\nmolecules form concentration gradients across tissues, thereby providing
    positional\r\ninformation that instructs the pattern of cell differentiation.
    Morphogen gradients are highly\r\ndynamic in space and time. Many factors such
    as morphogen production, spreading,\r\ndegradation, cellular rearrangements and
    others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal
    signalling dynamics arise in many systems is still unclear.\r\nWe studied the
    dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate
    neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes
    are specified in a spatially and temporally ordered manner in response to dorsal-toventral
    gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished
    and interpreted to ensure ordered cell specification is poorly understood.\r\nTo
    address this question, we developed a 2D embryonic stem cell differentiation system
    that\r\ncaptures key features of dorsal neural tube development. In this system,
    differentiated\r\ncolonies display remarkable self-organised pattern formation
    in response to uniformly\r\napplied BMP ligand. We established a method of differentiating
    the colonies using\r\nmicrofabricated stencils, which allowed us to control the
    initial size and shape of colonies\r\nwithout confining cell migration and colony
    growth. This led to highly reproducible pattern\r\nformation that facilitates
    quantification.\r\nUsing this approach, we observed striking two-phase temporal
    dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from
    the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established
    again in the second phase. By combining our\r\nquantitative data with a data-driven
    theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this
    biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled
    by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial
    response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation
    of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype
    pattern. The second phase is controlled by slow positive regulation of BMP signalling
    by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity.
    WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether,
    the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental
    events, making pattern formation spatially and temporally organised.\r\nFurthermore,
    this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts
    – first for the establishment of the neural plate border, and subsequently for
    dorsal\r\nneural progenitor patterning. Our study supports a general developmental
    principle in which\r\nmultiple morphogens interact with transcriptional networks
    resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive
    organised pattern formation."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
acknowledgement: "My work would also not have been possible without the Imaging and
  Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has
  facilitated my research substantially. I\r\nalso want to thank the Graduate School
  Office for their never-ending support and their sincere\r\neffort to improve the
  PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft
  für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank
  you for recognizing the importance of this project."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stefanie
  full_name: Rus, Stefanie
  id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
  last_name: Rus
  orcid: 0000-0001-8703-1093
citation:
  ama: Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal
    neural tube. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19763">10.15479/AT-ISTA-19763</a>
  apa: Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions
    in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a
    href="https://doi.org/10.15479/AT-ISTA-19763">https://doi.org/10.15479/AT-ISTA-19763</a>
  chicago: Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions
    in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025.
    <a href="https://doi.org/10.15479/AT-ISTA-19763">https://doi.org/10.15479/AT-ISTA-19763</a>.
  ieee: S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal
    neural tube,” Institute of Science and Technology Austria, 2025.
  ista: Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the
    dorsal neural tube. Institute of Science and Technology Austria.
  mla: Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions
    in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025,
    doi:<a href="https://doi.org/10.15479/AT-ISTA-19763">10.15479/AT-ISTA-19763</a>.
  short: S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal
    Neural Tube, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-05-30T09:14:58Z
date_published: 2025-05-29T00:00:00Z
date_updated: 2026-11-11T10:12:10Z
day: '29'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: AnKi
- _id: GradSch
doi: 10.15479/AT-ISTA-19763
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language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: '129'
project:
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
  grant_number: SC19-011
  name: The regulatory logic of pattern formation in the vertebrate dorsal neural
    tube
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '13136'
    relation: part_of_dissertation
    status: public
  - id: '17148'
    relation: part_of_dissertation
    status: public
  - id: '18807'
    relation: part_of_dissertation
    status: public
  - id: '18601'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
title: Dynamics of morphogen signalling and cell fate decisions in the dorsal neural
  tube
tmp:
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  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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  short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18807'
abstract:
- lang: eng
  text: Developing tissues interpret dynamic changes in morphogen activity to generate
    cell type diversity. To quantitatively study bone morphogenetic protein (BMP)
    signaling dynamics in the mouse neural tube, we developed an embryonic stem cell
    differentiation system tailored for growing tissues. Differentiating cells form
    striking self-organized patterns of dorsal neural tube cell types driven by sequential
    phases of BMP signaling that are observed both in vitro and in vivo. Data-driven
    biophysical modeling showed that these dynamics result from coupling fast negative
    feedback with slow positive regulation of signaling by the specification of an
    endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling
    in space, we identify a BMP signaling relay that operates in time. This mechanism
    allows for a rapid initial concentration-sensitive response that is robustly terminated,
    thereby regulating balanced sequential cell type generation. Our study provides
    an experimental and theoretical framework to understand how signaling dynamics
    are exploited in developing tissues.
acknowledgement: We thank A. Miller and N. Papalopulu for reagents and J. Briscoe
  for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European
  Research Council under Horizon Europe, grant 101044579; and the Austrian Science
  Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft
  für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was
  supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral
  Fellowship (ALTF 343-2022).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Stefanie
  full_name: Rus, Stefanie
  id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
  last_name: Rus
  orcid: 0000-0001-8703-1093
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Thomas
  full_name: Minchington, Thomas
  id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
  last_name: Minchington
- first_name: Martina
  full_name: Greunz, Martina
  id: 48A59534-F248-11E8-B48F-1D18A9856A87
  last_name: Greunz
- first_name: Jack
  full_name: Merrin, Jack
  id: 4515C308-F248-11E8-B48F-1D18A9856A87
  last_name: Merrin
  orcid: 0000-0001-5145-4609
- 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: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
citation:
  ama: Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in
    the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental
    Cell</i>. 2025;60(4):567-580. doi:<a href="https://doi.org/10.1016/j.devcel.2024.10.024">10.1016/j.devcel.2024.10.024</a>
  apa: Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E.
    B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing
    mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>.
    Cell Press. <a href="https://doi.org/10.1016/j.devcel.2024.10.024">https://doi.org/10.1016/j.devcel.2024.10.024</a>
  chicago: Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack
    Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation
    in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental
    Cell</i>. Cell Press, 2025. <a href="https://doi.org/10.1016/j.devcel.2024.10.024">https://doi.org/10.1016/j.devcel.2024.10.024</a>.
  ieee: S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing
    mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>,
    vol. 60, no. 4. Cell Press, pp. 567–580, 2025.
  ista: Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva
    A. 2025. Self-organized pattern formation in the developing mouse neural tube
    by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.
  mla: Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse
    Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>,
    vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:<a href="https://doi.org/10.1016/j.devcel.2024.10.024">10.1016/j.devcel.2024.10.024</a>.
  short: S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo,
    A. Kicheva, Developmental Cell 60 (2025) 567–580.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: RNA-seq data has been deposited at GEO and are publicly
  available as of the date of publication. Accession numbers are listed in the key
  resources table. Code for the quantification of fluorescence intensity (FI) profiles
  in differentiated cells on stencils, as well as for model simulations, is available
  on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390
date_created: 2025-01-09T11:25:47Z
date_published: 2025-02-24T00:00:00Z
date_updated: 2026-11-14T23:31:20Z
day: '24'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
- _id: NanoFab
doi: 10.1016/j.devcel.2024.10.024
external_id:
  isi:
  - '001434279000001'
  pmid:
  - '39603235'
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intvolume: '        60'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 567-580
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
  grant_number: '101044579'
  name: Mechanisms of tissue size regulation in spinal cord development
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
  grant_number: F7802
  name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
    control of growth and pattern in the spinal cord
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
  grant_number: SC19-011
  name: The regulatory logic of pattern formation in the vertebrate dorsal neural
    tube
publication: Developmental Cell
publication_identifier:
  issn:
  - 1534-5807
publication_status: published
publisher: Cell Press
quality_controlled: '1'
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status: public
supplementarymaterial: yes
title: Self-organized pattern formation in the developing mouse neural tube by a temporal
  relay of BMP signaling
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: 60
year: '2025'
...
---
OA_place: publisher
_id: '20485'
abstract:
- lang: eng
  text: "Neurons communicate with each other via chemical and electrical synapses.
    While \r\nmuch attention has been devoted to understanding the molecular players
    involved in \r\nchemical neurotransmission, the biology of gap junctions mediating
    electrical \r\ncommunication is understudied. This imbalance is not for their
    lack of significance – \r\nelectrical synapses make up about 20% of neuronal connections
    in different species \r\nfrom invertebrates to vertebrates, but rather reflects
    technical constraints and \r\ninvestigator bias. Many regard electrical synapses
    as simple channels, and much of \r\nwhat is known about them comes from studies
    on cell culture models. Insights into \r\ntheir in vivo biology are just starting
    to emerge.  \r\nThe channels of electrical synapses in most animals are formed
    by innexins. \r\nChordates are an exception: their electrical synapses consist
    of connexins. Even \r\nthough at the level of primary sequence innexins and connexins
    appear to be \r\nunrelated, structurally and functionally they have much in common.
    The nematode \r\nCaenorhabditis elegans is a promising model to study the biology
    of electrical \r\nsynapses. This animal offers a powerful toolbox to study neuron
    function at the \r\nmolecular, cell biological and physiological levels. It also
    offers a detailed connectome \r\nmap of all of its 302 neurons. The implications
    from studies of molecular pathways in \r\nC. elegans go beyond this organism,
    since ~80% of the nematode’s proteins have \r\nhuman homologs.  \r\nThis work
    aims to enhance our understanding of the in vivo biology of gap junctions \r\nusing
    C. elegans as a model. Using a proximity labelling approach, we profiled the \r\ninteractomes
    of two innexins that are expressed predominantly in neurons: UNC-7 and \r\nUNC-9.
    We identified scores of proteins that may have important roles for these \r\ninnexins
    and their electrical synapses. Using localization and functional assays to \r\nvalidate
    and further probe our findings, both at the whole-organism and the single-cell
    \r\nlevel, we found that gap junctions have heterogeneous protein compositions.
    Our \r\nfindings imply that electrical synapses are sophisticated, molecularly
    diverse \r\nstructures.  "
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "I would also like to acknowledge the funding that I received from
  the European Union’s\r\nHorizon 2020 research and Innovation programme under the
  Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been
  possible without the contribution and support of people\r\nbehind the scientific
  service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility
  (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit.
  I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC)
  Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michaela
  full_name: Misova, Michaela
  id: 495A3C32-F248-11E8-B48F-1D18A9856A87
  last_name: Misova
  orcid: 0000-0003-2427-6856
citation:
  ama: Misova M. Dissecting gap junction biology using the C. elegans nervous system.
    2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20485">10.15479/AT-ISTA-20485</a>
  apa: Misova, M. (2025). <i>Dissecting gap junction biology using the C. elegans
    nervous system</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-20485">https://doi.org/10.15479/AT-ISTA-20485</a>
  chicago: Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans
    Nervous System.” Institute of Science and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT-ISTA-20485">https://doi.org/10.15479/AT-ISTA-20485</a>.
  ieee: M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,”
    Institute of Science and Technology Austria, 2025.
  ista: Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous
    system. Institute of Science and Technology Austria.
  mla: Misova, Michaela. <i>Dissecting Gap Junction Biology Using the C. Elegans Nervous
    System</i>. Institute of Science and Technology Austria, 2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-20485">10.15479/AT-ISTA-20485</a>.
  short: M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System,
    Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-17T16:15:09Z
date_published: 2025-10-23T00:00:00Z
date_updated: 2026-11-13T09:57:29Z
day: '23'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaDe
doi: 10.15479/AT-ISTA-20485
doi_confirm: '1'
ec_funded: 1
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language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '155'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication_identifier:
  isbn:
  - 978-3-99078-068-8
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Mario
  full_name: de Bono, Mario
  id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
  last_name: de Bono
  orcid: 0000-0001-8347-0443
title: Dissecting gap junction biology using the C. elegans nervous system
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '20393'
abstract:
- lang: eng
  text: "During vertebrate development, the morphogen Sonic Hedgehog (Shh) plays a
    key role in \r\npatterning the tissues of the extending body. This requires precise
    coordination between the \r\nsize of the source of Shh production and the embryo
    body. Shh is produced by the notochord, \r\nas well as floorplate of the neural
    tube. In this thesis, we investigated how the sizes of the \r\nnotochord and floorplate
    are regulated and how they impact the developing mouse embryo.  \r\nTo measure
    the size and shape of the developing mouse notochord and the cell behaviours \r\nwithin
    this organ, we performed high-resolution measurements in cleared embryos between
    \r\nE8.5 and E10.5 of development. Strikingly, our data revealed that the notochord
    maintains a \r\nconstant cross-sectional area throughout the trunk over time as
    it lengthens by cell \r\nproliferation. We show that this is achieved by a feedback
    between the notochord cell \r\nproliferation rate and both the cross-sectional
    area of the trunk notochord and elongation of \r\nthe embryo. Using live imaging,
    we further show that notochord cells undergo posteriorly\r\ndirected active cell
    migration and that this cell migration contributes to maintaining the \r\nstructural
    integrity of the notochord. Our results show a complex coordination of cell \r\nbehaviours
    that allow for robust notochord morphogenesis during mouse development and \r\nthe
    maintenance of a defined Shh source size.  \r\nShh produced by the notochord induces
    a secondary Shh-producing domain, the floor plate. \r\nHow the notochord and floor
    plate contribute to the formation of the Shh gradient in the \r\nneural tube and
    to the regulation of the floor plate size is poorly understood. Our theoretical
    \r\nand experimental analysis indicates that only the initial levels of notochord-derived
    Shh \r\ninfluence the size of the floor plate, and the floor plate is insensitive
    to its own production of \r\nShh. After its initial establishment, the floor plate
    expands by tissue growth, leading to scaling \r\nof the Shh gradient amplitude
    with tissue size.   \r\nAltogether, we show that the mechanisms regulating the
    sizes of the notochord and \r\nfloorplate in mouse development help to achieve
    size robustness of these tissues. Our data \r\ndemonstrate that the initial establishment
    of the Shh gradient in the neural tube is strongly \r\ndependent on the notochord
    and suggest that the robustness of notochord morphogenesis \r\nis essential for
    pattern formation. Later in development, the floor plate size and the Shh \r\ngradient
    are coupled to neural tube growth. Our findings provide new insights on how pattern
    \r\nformation, tissue growth and morphogenesis interact to ensure reproducible
    developmental \r\noutcomes. "
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kasumi
  full_name: Kishi, Kasumi
  id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
  last_name: Kishi
  orcid: 0000-0001-6060-4795
citation:
  ama: Kishi K. Regulation of notochord and floor plate size during mouse development.
    2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20393">10.15479/AT-ISTA-20393</a>
  apa: Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse
    development</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-20393">https://doi.org/10.15479/AT-ISTA-20393</a>
  chicago: Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse
    Development.” Institute of Science and Technology Austria, 2025. <a href="https://doi.org/10.15479/AT-ISTA-20393">https://doi.org/10.15479/AT-ISTA-20393</a>.
  ieee: K. Kishi, “Regulation of notochord and floor plate size during mouse development,”
    Institute of Science and Technology Austria, 2025.
  ista: Kishi K. 2025. Regulation of notochord and floor plate size during mouse development.
    Institute of Science and Technology Austria.
  mla: Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse
    Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-20393">10.15479/AT-ISTA-20393</a>.
  short: K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development,
    Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-09-25T10:08:10Z
date_published: 2025-09-24T00:00:00Z
date_updated: 2026-11-11T10:11:08Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: AnKi
- _id: EdHa
doi: 10.15479/AT-ISTA-20393
doi_confirm: '1'
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fulldoi: https://doi.org/10.15479/AT-ISTA-20393
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '102'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '18481'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
title: Regulation of notochord and floor plate size during mouse development
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
_id: '19557'
abstract:
- lang: eng
  text: "Numerous studies have revealed a wide range of genes associated with autism
    \r\nspectrum disorder (ASD), raising critical questions about how mutations across
    \r\ndifferent genes lead to similar clinical presentations. Yet, specific molecular
    \r\nmechanisms underlying most ASD cases remain elusive. Notably, ASD is diagnosed
    \r\nfour times more frequently in males than in females, highlighting a substantial
    sex \r\ndisparity. This male predominance is among the most recognized but least
    understood \r\ncharacteristics of the disorder. Thus, uncovering molecular mechanisms
    involved is \r\ncrucial for exploring both shared and distinct aspects of ASD.
    \ \r\nWe utilized single-nucleus multi-omics sequencing to explore these unresolved
    \r\nquestions, enabling us to investigate changes in gene expression and chromatin
    \r\naccessibility concurrently. In the present work, we analyzed and compared
    251 \r\nsamples collected from eleven different monogenic mouse models of ASD,
    \r\nincorporating both sexes and two brain regions. Samples span three primary
    \r\ndevelopmental stages, which include prenatal, early postnatal, and juvenile
    brain \r\ndevelopment. This comprehensive dataset allowed us to map functional
    mechanisms \r\nspecific to cell states, sex, and developmental periods. \r\nWe
    discovered that ASD mutations commonly delay the progression of radial glial \r\ncells,
    temporarily affecting the neural lineage specification. The most notable gene
    \r\nexpression changes occurred perinatally, mainly affecting excitatory and inhibitory
    \r\nneurons. These alterations involved a downregulation of genes related to synapses
    \r\nand ion channels, indicating possible homeostatic adaptations. While there
    were \r\nseveral common molecular changes across all models, each mutant also
    displayed \r\nunique states.  \r\nThroughout the perinatal phase, numerous processes
    of cortical regulation and \r\nrefinement take place. At this stage, several ASD
    risk genes exhibit a common set of \r\ndifferentially expressed genes, converging
    on a subclass of dysregulated \r\nmechanisms. However, as cortical development
    progresses, these shared processes \r\nstart to diverge. This suggests that the
    period around P4 represents a critical time \r\nwindow for many converging molecular
    processes, marking it as the most impacted \r\nstage. \r\nImportantly, our study
    highlighted sex-specific gene expression alterations, with \r\nfemales often showing
    broader dysregulations and larger effect sizes compared to \r\nmales.  \r\nIn
    contrast to the cerebral cortex, the cerebellum showed fewer gene expression \r\nchanges
    across most ASD mutant models, with the exception of one mutant that \r\nshowed
    consistent alterations in both brain regions.  \r\nOverall, our findings provide
    a thorough view of the cellular and molecular dynamics \r\nin different ASD models,
    highlighting both common and unique features across \r\ndifferent genetic backgrounds.
    By exploring multiple genetic forms of ASD, we could \r\ndemonstrate the dynamic
    nature of ASD-related changes in the brain and emphasize \r\nthe importance of
    accounting for sex-dependent factors. In conclusion, this work \r\nserves as a
    valuable multi-omics resource, providing a foundation for future \r\ninvestigations. "
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: ScienComp
acknowledgement: "The work presented in this doctoral thesis was performed at the
  Institute of Science\r\nand Technology (ISTA) and financially supported by a European
  Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02)
  and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very
  thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering
  me financial\r\nsupport to perform essential experiments during my PhD studies and
  to participate in\r\ninternational conferences and courses."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lena A
  full_name: Schwarz, Lena A
  id: 29A8453C-F248-11E8-B48F-1D18A9856A87
  last_name: Schwarz
citation:
  ama: Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse
    models at single-cell resolution. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19557">10.15479/AT-ISTA-19557</a>
  apa: Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum
    disorder mouse models at single-cell resolution</i>. Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/AT-ISTA-19557">https://doi.org/10.15479/AT-ISTA-19557</a>
  chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder
    Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria,
    2025. <a href="https://doi.org/10.15479/AT-ISTA-19557">https://doi.org/10.15479/AT-ISTA-19557</a>.
  ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder
    mouse models at single-cell resolution,” Institute of Science and Technology Austria,
    2025.
  ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder
    mouse models at single-cell resolution. Institute of Science and Technology Austria.
  mla: Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder
    Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology
    Austria, 2025, doi:<a href="https://doi.org/10.15479/AT-ISTA-19557">10.15479/AT-ISTA-19557</a>.
  short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder
    Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria,
    2025.
corr_author: '1'
date_created: 2025-04-14T06:59:06Z
date_published: 2025-04-14T00:00:00Z
date_updated: 2026-11-13T12:31:10Z
day: '14'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GaNo
doi: 10.15479/AT-ISTA-19557
doi_confirm: '1'
file:
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fulldoi: https://doi.org/10.15479/AT-ISTA-19557
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 9B91375C-BA93-11EA-9121-9846C619BF3A
  grant_number: '707964'
  name: Critical windows and reversibility of ASD associated with mutations in chromatin
    remodelers
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
  grant_number: '101044865'
  name: Toward an understanding of the brain interstitial system and the extracellular
    proteome in health and autism spectrum disorders
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '12802'
    relation: part_of_dissertation
    status: public
  - id: '9429'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
title: Mapping developmental dynamics of autism spectrum disorder mouse models at
  single-cell resolution
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21064'
abstract:
- lang: eng
  text: The James Webb Space Telescope (JWST) is revolutionizing our knowledge of
    z > 5 galaxies and their actively accreting black holes. Using the JWST Cycle
    1 Treasury program Ultradeep NIRSpec and NIRCam Observations before the Epoch
    of Reionization (UNCOVER) in the lensing field A2744, we report the identification
    of a sample of little red dots at 3 < zphot < 7 that likely contain highly reddened
    accreting supermassive black holes. Using a NIRCam-only selection to F444W < 27.7
    mag, we find 26 sources over the ∼45 arcmin^2 field that are blue in F115W − F200W
    ∼ 0 (or βUV ∼ –2.0 for fλ ∝ λ^β), red in F200W − F444W = 1−4 (βopt ∼ +2.0), and
    are dominated by a point-source-like central component. Of the 20 sources with
    deep Atacama Large Millimeter/submillimeter Array (ALMA) 1.2 mm coverage, none
    are detected individually or in a stack. For the majority of the sample, spectral
    energy distribution fits to the JWST+ALMA observations prefer models with hot
    dust rather than obscured star formation to reproduce the red NIRCam colors and
    ALMA 1.2 mm nondetections. While compact dusty star formation cannot be ruled
    out, the combination of extremely small sizes (〈re〉 ≈ 50 pc after correction for
    magnification), red rest-frame optical slopes, and hot dust can be explained by
    reddened broad-line active galactic nuclei (AGNs). Our targets have faint M1450
    ≈ −14 to −18 mag but inferred bolometric luminosities of Lbol = 10^43–10^46 erg
    s^−1, reflecting their obscured nature. If the candidates are confirmed as AGNs
    with upcoming UNCOVER spectroscopy, then we have found an abundant population
    of reddened luminous AGNs that are at least ten times more numerous than UV-luminous
    AGNs at the same intrinsic bolometric luminosity.
acknowledgement: 'I.L. acknowledges support from Australian Research Council Future
  Fellowship FT220100798. J.E.G. and A.D.G acknowledge support from NSF/AAG grant
  #1007094, and J.E.G. also acknowledges support from NSF/AAG grant #1007052. L.J.F.
  and A.Z. acknowledge support by Grant No. 2020750 from the United States–Israel
  Binational Science Foundation (BSF) and grant No. 2109066 from the United States
  National Science Foundation (NSF), and by the Ministry of Science & Technology of
  Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation
  (DNRF) under grant #140. This 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. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (“ODIN”)
  and from the European Commission’s and University of Groningen’s CO-FUND Rosalind
  Franklin program. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279.
  Support for this work was provided by NASA through the NASA Hubble Fellowship grant
  HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated
  by the Association of Universities for Research in Astronomy, Incorporated, under
  NASA contract NAS5-26555. This paper makes use of the ALMA data: ADS/JAO. ALMA #2022.1.00073.S,
  2018.1.00035.L, and 2013.1.00999.S. ALMA is a partnership of ESO (representing its
  member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and
  ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of
  Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The research
  of C.C.W. 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.'
article_number: '92'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Ivo
  full_name: Labbe, Ivo
  last_name: Labbe
- first_name: Jenny E.
  full_name: Greene, Jenny E.
  last_name: Greene
- first_name: Rachel
  full_name: Bezanson, Rachel
  last_name: Bezanson
- first_name: Seiji
  full_name: Fujimoto, Seiji
  last_name: Fujimoto
- first_name: Lukas J.
  full_name: Furtak, Lukas J.
  last_name: Furtak
- first_name: Andy D.
  full_name: Goulding, Andy D.
  last_name: Goulding
- 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: Rohan P.
  full_name: Naidu, Rohan P.
  last_name: Naidu
- first_name: Pascal A.
  full_name: Oesch, Pascal A.
  last_name: Oesch
- first_name: Hakim
  full_name: Atek, Hakim
  last_name: Atek
- first_name: Gabriel
  full_name: Brammer, Gabriel
  last_name: Brammer
- first_name: Iryna
  full_name: Chemerynska, Iryna
  last_name: Chemerynska
- first_name: Dan
  full_name: Coe, Dan
  last_name: Coe
- first_name: Sam E.
  full_name: Cutler, Sam E.
  last_name: Cutler
- first_name: Pratika
  full_name: Dayal, Pratika
  last_name: Dayal
- first_name: Robert
  full_name: Feldmann, Robert
  last_name: Feldmann
- first_name: Marijn
  full_name: Franx, Marijn
  last_name: Franx
- first_name: Karl
  full_name: Glazebrook, Karl
  last_name: Glazebrook
- first_name: Joel
  full_name: Leja, Joel
  last_name: Leja
- first_name: Michael
  full_name: Maseda, Michael
  last_name: Maseda
- first_name: Danilo
  full_name: Marchesini, Danilo
  last_name: Marchesini
- first_name: Themiya
  full_name: Nanayakkara, Themiya
  last_name: Nanayakkara
- first_name: Erica J.
  full_name: Nelson, Erica J.
  last_name: Nelson
- first_name: Richard
  full_name: Pan, Richard
  last_name: Pan
- first_name: Casey
  full_name: Papovich, Casey
  last_name: Papovich
- first_name: Sedona H.
  full_name: Price, Sedona H.
  last_name: Price
- first_name: Katherine A.
  full_name: Suess, Katherine A.
  last_name: Suess
- first_name: Bingjie 冰洁
  full_name: Wang, Bingjie 冰洁
  last_name: Wang
- first_name: John R.
  full_name: Weaver, John R.
  last_name: Weaver
- first_name: Katherine E.
  full_name: Whitaker, Katherine E.
  last_name: Whitaker
- first_name: Christina C.
  full_name: Williams, Christina C.
  last_name: Williams
- first_name: Adi
  full_name: Zitrin, Adi
  last_name: Zitrin
citation:
  ama: 'Labbe I, Greene JE, Bezanson R, et al. UNCOVER: Candidate red active galactic
    nuclei at 3 &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>.
    2024;978. doi:<a href="https://doi.org/10.3847/1538-4357/ad3551">10.3847/1538-4357/ad3551</a>'
  apa: 'Labbe, I., Greene, J. E., Bezanson, R., Fujimoto, S., Furtak, L. J., Goulding,
    A. D., … Zitrin, A. (2024). UNCOVER: Candidate red active galactic nuclei at 3
    &#60; z &#60; 7 with JWST and ALMA. <i>The Astrophysical Journal</i>. IOP Publishing.
    <a href="https://doi.org/10.3847/1538-4357/ad3551">https://doi.org/10.3847/1538-4357/ad3551</a>'
  chicago: 'Labbe, Ivo, Jenny E. Greene, Rachel Bezanson, Seiji Fujimoto, Lukas J.
    Furtak, Andy D. Goulding, Jorryt J Matthee, et al. “UNCOVER: Candidate Red Active
    Galactic Nuclei at 3 &#60; z &#60; 7 with JWST and ALMA.” <i>The Astrophysical
    Journal</i>. IOP Publishing, 2024. <a href="https://doi.org/10.3847/1538-4357/ad3551">https://doi.org/10.3847/1538-4357/ad3551</a>.'
  ieee: 'I. Labbe <i>et al.</i>, “UNCOVER: Candidate red active galactic nuclei at
    3 &#60; z &#60; 7 with JWST and ALMA,” <i>The Astrophysical Journal</i>, vol.
    978. IOP Publishing, 2024.'
  ista: 'Labbe I, Greene JE, Bezanson R, Fujimoto S, Furtak LJ, Goulding AD, Matthee
    JJ, Naidu RP, Oesch PA, Atek H, Brammer G, Chemerynska I, Coe D, Cutler SE, Dayal
    P, Feldmann R, Franx M, Glazebrook K, Leja J, Maseda M, Marchesini D, Nanayakkara
    T, Nelson EJ, Pan R, Papovich C, Price SH, Suess KA, Wang B冰洁, Weaver JR, Whitaker
    KE, Williams CC, Zitrin A. 2024. UNCOVER: Candidate red active galactic nuclei
    at 3 &#60; z &#60; 7 with JWST and ALMA. The Astrophysical Journal. 978, 92.'
  mla: 'Labbe, Ivo, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 &#60;
    z &#60; 7 with JWST and ALMA.” <i>The Astrophysical Journal</i>, vol. 978, 92,
    IOP Publishing, 2024, doi:<a href="https://doi.org/10.3847/1538-4357/ad3551">10.3847/1538-4357/ad3551</a>.'
  short: I. Labbe, J.E. Greene, R. Bezanson, S. Fujimoto, L.J. Furtak, A.D. Goulding,
    J.J. Matthee, R.P. Naidu, P.A. Oesch, H. Atek, G. Brammer, I. Chemerynska, D.
    Coe, S.E. Cutler, P. Dayal, R. Feldmann, M. Franx, K. Glazebrook, J. Leja, M.
    Maseda, D. Marchesini, T. Nanayakkara, E.J. Nelson, R. Pan, C. Papovich, S.H.
    Price, K.A. Suess, B.冰洁 Wang, J.R. Weaver, K.E. Whitaker, C.C. Williams, A. Zitrin,
    The Astrophysical Journal 978 (2024).
date_created: 2026-01-28T15:26:12Z
date_published: 2024-12-26T00:00:00Z
date_updated: 2026-02-10T06:49:49Z
day: '26'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.3847/1538-4357/ad3551
external_id:
  arxiv:
  - '2306.07320'
file:
- access_level: open_access
  checksum: 825c35ebd26e292c8a5c2bffac327854
  content_type: application/pdf
  creator: dernst
  date_created: 2026-02-10T06:44:24Z
  date_updated: 2026-02-10T06:44:24Z
  file_id: '21201'
  file_name: 2024_AstrophysicalJourn_Labbe.pdf
  file_size: 5041924
  relation: main_file
  success: 1
file_date_updated: 2026-02-10T06:44:24Z
fulldoi: https://doi.org/10.3847/1538-4357/ad3551
has_accepted_license: '1'
intvolume: '       978'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
  eissn:
  - 1538-4357
  issn:
  - 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA'
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: 978
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '21304'
abstract:
- lang: eng
  text: No description provided.
article_processing_charge: No
author:
- first_name: Miguel
  full_name: Santana de Freitas Amaral, Miguel
  id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501
  last_name: Santana de Freitas Amaral
citation:
  ama: 'Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024.
    doi:<a href="https://doi.org/10.5281/ZENODO.13934991">10.5281/ZENODO.13934991</a>'
  apa: 'Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples.
    Zenodo. <a href="https://doi.org/10.5281/ZENODO.13934991">https://doi.org/10.5281/ZENODO.13934991</a>'
  chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.”
    Zenodo, 2024. <a href="https://doi.org/10.5281/ZENODO.13934991">https://doi.org/10.5281/ZENODO.13934991</a>.'
  ieee: 'M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo,
    2024.'
  ista: 'Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples,
    Zenodo, <a href="https://doi.org/10.5281/ZENODO.13934991">10.5281/ZENODO.13934991</a>.'
  mla: 'Santana de Freitas Amaral, Miguel. <i>Archaeal_membranes : Code and Examples</i>.
    Zenodo, 2024, doi:<a href="https://doi.org/10.5281/ZENODO.13934991">10.5281/ZENODO.13934991</a>.'
  short: M. Santana de Freitas Amaral, (2024).
corr_author: '1'
date_created: 2026-02-17T12:52:26Z
date_published: 2024-10-15T00:00:00Z
date_updated: 2026-02-23T11:49:05Z
day: '15'
department:
- _id: AnSa
doi: 10.5281/ZENODO.13934991
fulldoi: https://doi.org/10.5281/ZENODO.13934991
has_accepted_license: '1'
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5281/ZENODO.13934991
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
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  - id: '21251'
    relation: used_for_analysis_in
    status: public
status: public
title: 'archaeal_membranes : code and examples'
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_type: green
_id: '21967'
abstract:
- lang: eng
  text: "Selection against deleterious mutations, called purifying selection, plays
    a central role in evolution and acts in all populations. It is known that the
    genetic patterns observed in genomic regions undergoing purifying selection differ
    from those resulting from neutral evolution. However, a comprehensive understanding
    of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn
    the present work, we use simulations combined with a genealogical approach to
    identify the effect of purifying selection on the ancestry and thus on the genetic
    diversity. Our analysis relies on the postulate that the genealogy belongs to
    the universality class of Beta-coalescents. Under this assumption, we derive statistics
    measuring the distortion of the genealogy. This approach allows us to consider
    a wide range of regimes (i.e. arbitrary selection and mutation strengths) and
    uncover a rich phase diagram. We find that, for strong selection, the limiting
    genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection
    gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple
    mergers in the genealogical structures. Our results show that while multiple-merger
    coalescents are often interpreted as the signature of selective sweeps in rapidly
    adapting populations, these structures can also appear in the context of Muller’s
    ratchet."
acknowledgement: This work was supported by the Austrian Academy of Science, DOC fellowship
  No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme
  under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations
  were performed on the ISTA High-performance Computing Cluster.
article_processing_charge: No
author:
- first_name: Kseniia
  full_name: Khudiakova, Kseniia
  id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
  last_name: Khudiakova
  orcid: 0000-0002-6246-1465
- first_name: Florin
  full_name: Boenkost, Florin
  last_name: Boenkost
- first_name: Julie N
  full_name: Tourniaire, Julie N
  id: 5dc06dd8-8e51-11ec-9170-8d9c450cc216
  last_name: Tourniaire
citation:
  ama: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection.
    <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2024.10.15.618444">10.1101/2024.10.15.618444</a>
  apa: Khudiakova, K., Boenkost, F., &#38; Tourniaire, J. N. (n.d.). Genealogies under
    purifying selection. <i>bioRxiv</i>. <a href="https://doi.org/10.1101/2024.10.15.618444">https://doi.org/10.1101/2024.10.15.618444</a>
  chicago: Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies
    under Purifying Selection.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2024.10.15.618444">https://doi.org/10.1101/2024.10.15.618444</a>.
  ieee: K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying
    selection,” <i>bioRxiv</i>. .
  ista: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection.
    bioRxiv, <a href="https://doi.org/10.1101/2024.10.15.618444">10.1101/2024.10.15.618444</a>.
  mla: Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” <i>BioRxiv</i>,
    doi:<a href="https://doi.org/10.1101/2024.10.15.618444">10.1101/2024.10.15.618444</a>.
  short: K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-06-09T12:14:08Z
date_published: 2024-10-18T00:00:00Z
date_updated: 2026-06-12T12:43:34Z
day: '18'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2024.10.15.618444
ec_funded: 1
fulldoi: https://doi.org/10.1101/2024.10.15.618444
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2024.10.15.618444
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
  grant_number: '26293'
  name: The impact of deleterious mutations on small populations
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '21918'
    relation: dissertation_contains
    status: public
status: public
title: Genealogies under purifying selection
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '14543'
abstract:
- lang: eng
  text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed,
    plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation
    of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function
    in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology.
    Utilizing exome sequencing and extensive international data sharing efforts, we
    identified 45 affected individuals from 28 unrelated families (consanguinity 93%)
    with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in
    ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9
    and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical
    proteomics in the model organisms and human cells, with the latter also being
    subjected further to ACBD6 peroxisomal localization studies. The affected individuals
    (23 males and 22 females), with ages ranging from 1 to 50 years old, typically
    present with a complex and progressive disease involving moderate-to-severe global
    developmental delay/intellectual disability (100%) with significant expressive
    language impairment (98%), movement disorders (97%), facial dysmorphism (95%),
    and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia
    (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%),
    microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement
    disorder was dystonia (94%), frequently leading to early-onset progressive postural
    deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor
    in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing
    with advancing age (32%), and simple motor and vocal tics were among other frequent
    movement disorders. Midline brain malformations including corpus callosum abnormalities
    (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and
    small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava
    (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus
    models effectively recapitulated many clinical phenotypes reported in patients
    including movement disorders, progressive neuromotor impairment, seizures, microcephaly,
    craniofacial dysmorphism, and midbrain defects accompanied by developmental delay
    with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal
    localisation and ACBD6-deficiency was not associated with altered peroxisomal
    parameters in patient fibroblasts. Significant differences in YnMyr-labelling
    were observed for 68 co- and 18 post-translationally N-myristoylated proteins
    in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient
    zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related
    proteins implicated in neurological diseases. The present study provides evidence
    that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental
    syndrome accompanied by complex and progressive cognitive and movement disorders.
article_processing_charge: No
article_type: original
author:
- first_name: Rauan
  full_name: Kaiyrzhanov, Rauan
  last_name: Kaiyrzhanov
- first_name: Aboulfazl
  full_name: Rad, Aboulfazl
  last_name: Rad
- first_name: Sheng-Jia
  full_name: Lin, Sheng-Jia
  last_name: Lin
- first_name: Aida
  full_name: Bertoli-Avella, Aida
  last_name: Bertoli-Avella
- first_name: Wouter W
  full_name: Kallemeijn, Wouter W
  last_name: Kallemeijn
- first_name: Annie
  full_name: Godwin, Annie
  last_name: Godwin
- first_name: Maha S
  full_name: Zaki, Maha S
  last_name: Zaki
- first_name: Kevin
  full_name: Huang, Kevin
  id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3
  last_name: Huang
  orcid: 0000-0002-2512-7812
- first_name: Tracy
  full_name: Lau, Tracy
  last_name: Lau
- first_name: Cassidy
  full_name: Petree, Cassidy
  last_name: Petree
- first_name: Stephanie
  full_name: Efthymiou, Stephanie
  last_name: Efthymiou
- first_name: Ehsan
  full_name: Ghayoor Karimiani, Ehsan
  last_name: Ghayoor Karimiani
- first_name: Maja
  full_name: Hempel, Maja
  last_name: Hempel
- first_name: Elizabeth A
  full_name: Normand, Elizabeth A
  last_name: Normand
- first_name: Sabine
  full_name: Rudnik-Schöneborn, Sabine
  last_name: Rudnik-Schöneborn
- first_name: Ulrich A
  full_name: Schatz, Ulrich A
  last_name: Schatz
- first_name: Marc P
  full_name: Baggelaar, Marc P
  last_name: Baggelaar
- first_name: Muhammad
  full_name: Ilyas, Muhammad
  last_name: Ilyas
- first_name: Tipu
  full_name: Sultan, Tipu
  last_name: Sultan
- first_name: Javeria Raza
  full_name: Alvi, Javeria Raza
  last_name: Alvi
- first_name: Manizha
  full_name: Ganieva, Manizha
  last_name: Ganieva
- first_name: Ben
  full_name: Fowler, Ben
  last_name: Fowler
- first_name: Ruxandra
  full_name: Aanicai, Ruxandra
  last_name: Aanicai
- first_name: Gulsen
  full_name: Akay Tayfun, Gulsen
  last_name: Akay Tayfun
- first_name: Abdulaziz
  full_name: Al Saman, Abdulaziz
  last_name: Al Saman
- first_name: Abdulrahman
  full_name: Alswaid, Abdulrahman
  last_name: Alswaid
- first_name: Nafise
  full_name: Amiri, Nafise
  last_name: Amiri
- first_name: Nilufar
  full_name: Asilova, Nilufar
  last_name: Asilova
- first_name: Vorasuk
  full_name: Shotelersuk, Vorasuk
  last_name: Shotelersuk
- first_name: Patra
  full_name: Yeetong, Patra
  last_name: Yeetong
- first_name: Matloob
  full_name: Azam, Matloob
  last_name: Azam
- first_name: Meisam
  full_name: Babaei, Meisam
  last_name: Babaei
- first_name: Gholamreza
  full_name: Bahrami Monajemi, Gholamreza
  last_name: Bahrami Monajemi
- first_name: Pouria
  full_name: Mohammadi, Pouria
  last_name: Mohammadi
- first_name: Saeed
  full_name: Samie, Saeed
  last_name: Samie
- first_name: Selina Husna
  full_name: Banu, Selina Husna
  last_name: Banu
- first_name: Jorge Pinto
  full_name: Basto, Jorge Pinto
  last_name: Basto
- first_name: Fanny
  full_name: Kortüm, Fanny
  last_name: Kortüm
- first_name: Mislen
  full_name: Bauer, Mislen
  last_name: Bauer
- first_name: Peter
  full_name: Bauer, Peter
  last_name: Bauer
- first_name: Christian
  full_name: Beetz, Christian
  last_name: Beetz
- first_name: Masoud
  full_name: Garshasbi, Masoud
  last_name: Garshasbi
- first_name: Awatif
  full_name: Hameed Issa, Awatif
  last_name: Hameed Issa
- first_name: Wafaa
  full_name: Eyaid, Wafaa
  last_name: Eyaid
- first_name: Hind
  full_name: Ahmed, Hind
  last_name: Ahmed
- first_name: Narges
  full_name: Hashemi, Narges
  last_name: Hashemi
- first_name: Kazem
  full_name: Hassanpour, Kazem
  last_name: Hassanpour
- first_name: Isabella
  full_name: Herman, Isabella
  last_name: Herman
- first_name: Sherozjon
  full_name: Ibrohimov, Sherozjon
  last_name: Ibrohimov
- first_name: Ban A
  full_name: Abdul-Majeed, Ban A
  last_name: Abdul-Majeed
- first_name: Maria
  full_name: Imdad, Maria
  last_name: Imdad
- first_name: Maksudjon
  full_name: Isrofilov, Maksudjon
  last_name: Isrofilov
- first_name: Qassem
  full_name: Kaiyal, Qassem
  last_name: Kaiyal
- first_name: Suliman
  full_name: Khan, Suliman
  last_name: Khan
- first_name: Brian
  full_name: Kirmse, Brian
  last_name: Kirmse
- first_name: Janet
  full_name: Koster, Janet
  last_name: Koster
- first_name: Charles Marques
  full_name: Lourenço, Charles Marques
  last_name: Lourenço
- first_name: Tadahiro
  full_name: Mitani, Tadahiro
  last_name: Mitani
- first_name: Oana
  full_name: Moldovan, Oana
  last_name: Moldovan
- first_name: David
  full_name: Murphy, David
  last_name: Murphy
- first_name: Maryam
  full_name: Najafi, Maryam
  last_name: Najafi
- first_name: Davut
  full_name: Pehlivan, Davut
  last_name: Pehlivan
- first_name: Maria Eugenia
  full_name: Rocha, Maria Eugenia
  last_name: Rocha
- first_name: Vincenzo
  full_name: Salpietro, Vincenzo
  last_name: Salpietro
- first_name: Miriam
  full_name: Schmidts, Miriam
  last_name: Schmidts
- first_name: Adel
  full_name: Shalata, Adel
  last_name: Shalata
- first_name: Mohammad
  full_name: Mahroum, Mohammad
  last_name: Mahroum
- first_name: Jawabreh Kassem
  full_name: Talbeya, Jawabreh Kassem
  last_name: Talbeya
- first_name: Robert W
  full_name: Taylor, Robert W
  last_name: Taylor
- first_name: Dayana
  full_name: Vazquez, Dayana
  last_name: Vazquez
- first_name: Annalisa
  full_name: Vetro, Annalisa
  last_name: Vetro
- first_name: Hans R
  full_name: Waterham, Hans R
  last_name: Waterham
- first_name: Mashaya
  full_name: Zaman, Mashaya
  last_name: Zaman
- first_name: Tina A
  full_name: Schrader, Tina A
  last_name: Schrader
- first_name: Wendy K
  full_name: Chung, Wendy K
  last_name: Chung
- first_name: Renzo
  full_name: Guerrini, Renzo
  last_name: Guerrini
- first_name: James R
  full_name: Lupski, James R
  last_name: Lupski
- first_name: Joseph
  full_name: Gleeson, Joseph
  last_name: Gleeson
- first_name: Mohnish
  full_name: Suri, Mohnish
  last_name: Suri
- first_name: Yalda
  full_name: Jamshidi, Yalda
  last_name: Jamshidi
- first_name: Kailash P
  full_name: Bhatia, Kailash P
  last_name: Bhatia
- first_name: Barbara
  full_name: Vona, Barbara
  last_name: Vona
- first_name: Michael
  full_name: Schrader, Michael
  last_name: Schrader
- first_name: Mariasavina
  full_name: Severino, Mariasavina
  last_name: Severino
- first_name: Matthew
  full_name: Guille, Matthew
  last_name: Guille
- first_name: Edward W
  full_name: Tate, Edward W
  last_name: Tate
- first_name: Gaurav K
  full_name: Varshney, Gaurav K
  last_name: Varshney
- first_name: Henry
  full_name: Houlden, Henry
  last_name: Houlden
- first_name: Reza
  full_name: Maroofian, Reza
  last_name: Maroofian
citation:
  ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental
    syndrome with progressive and complex movement disorders. <i>Brain</i>. 2024;147(4):1436-1456.
    doi:<a href="https://doi.org/10.1093/brain/awad380">10.1093/brain/awad380</a>
  apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W.,
    Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental
    syndrome with progressive and complex movement disorders. <i>Brain</i>. Oxford
    University Press. <a href="https://doi.org/10.1093/brain/awad380">https://doi.org/10.1093/brain/awad380</a>
  chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella,
    Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants
    Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.”
    <i>Brain</i>. Oxford University Press, 2024. <a href="https://doi.org/10.1093/brain/awad380">https://doi.org/10.1093/brain/awad380</a>.
  ieee: R. Kaiyrzhanov <i>et al.</i>, “Bi-allelic ACBD6 variants lead to a neurodevelopmental
    syndrome with progressive and complex movement disorders,” <i>Brain</i>, vol.
    147, no. 4. Oxford University Press, pp. 1436–1456, 2024.
  ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A,
    Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M,
    Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi
    JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri
    N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G,
    Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C,
    Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman
    I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse
    B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D,
    Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW,
    Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski
    JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M,
    Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6
    variants lead to a neurodevelopmental syndrome with progressive and complex movement
    disorders. Brain. 147(4), 1436–1456.
  mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental
    Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>, vol.
    147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:<a href="https://doi.org/10.1093/brain/awad380">10.1093/brain/awad380</a>.
  short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A.
    Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani,
    M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M.
    Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun,
    A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M.
    Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P.
    Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa,
    W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed,
    M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço,
    T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro,
    M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A.
    Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski,
    J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino,
    M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024)
    1436–1456.
date_created: 2023-11-16T12:36:51Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2024-07-16T08:23:24Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1093/brain/awad380
extern: '1'
external_id:
  pmid:
  - '37951597'
file:
- access_level: open_access
  checksum: 0ee7a8ab9300225d60968f7a3e3cfa0d
  content_type: application/pdf
  creator: dernst
  date_created: 2024-07-16T08:22:13Z
  date_updated: 2024-07-16T08:22:13Z
  file_id: '17254'
  file_name: 2024_Brain_Kaiyrzhanov.pdf
  file_size: 2641456
  relation: main_file
  success: 1
file_date_updated: 2024-07-16T08:22:13Z
fulldoi: https://doi.org/10.1093/brain/awad380
has_accepted_license: '1'
intvolume: '       147'
issue: '4'
keyword:
- Neurology (clinical)
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 1436-1456
pmid: 1
publication: Brain
publication_identifier:
  eissn:
  - 1460-2156
  issn:
  - 0006-8950
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive
  and complex movement disorders
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: 147
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15379'
abstract:
- lang: eng
  text: Long-term potentiation (LTP) of excitatory synapses is a leading model to
    explain the concept of information storage in the brain. Multiple mechanisms contribute
    to LTP, but central amongst them is an increased sensitivity of the postsynaptic
    membrane to neurotransmitter release. This sensitivity is predominantly determined
    by the abundance and localization of AMPA-type glutamate receptors (AMPARs). A
    combination of AMPAR structural data, super-resolution imaging of excitatory synapses,
    and an abundance of electrophysiological studies are providing an ever-clearer
    picture of how AMPARs are recruited and organized at synaptic junctions. Here,
    we review the latest insights into this process, and discuss how both cytoplasmic
    and extracellular receptor elements cooperate to tune the AMPAR response at the
    hippocampal CA1 synapse.
acknowledgement: The authors thank Alexander Scrutton and James M. Krieger for comments
  on the manuscript. The authors also acknowledge Shraddha Nayak for help with Figure
  1B design. This work was supported by grants from the Medical Research Council (MC_U105174197),
  the BBSRC (BB/N002113/1), and the Wellcome Trust (223194/Z/21/Z) to IHG.
article_number: ' 2400006'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Imogen
  full_name: Stockwell, Imogen
  last_name: Stockwell
- first_name: Jake
  full_name: Watson, Jake
  id: 63836096-4690-11EA-BD4E-32803DDC885E
  last_name: Watson
  orcid: 0000-0002-8698-3823
- first_name: Ingo H.
  full_name: Greger, Ingo H.
  last_name: Greger
citation:
  ama: Stockwell I, Watson J, Greger IH. Tuning synaptic strength by regulation of
    AMPA glutamate receptor localization. <i>BioEssays</i>. 2024;46(7). doi:<a href="https://doi.org/10.1002/bies.202400006">10.1002/bies.202400006</a>
  apa: Stockwell, I., Watson, J., &#38; Greger, I. H. (2024). Tuning synaptic strength
    by regulation of AMPA glutamate receptor localization. <i>BioEssays</i>. Wiley.
    <a href="https://doi.org/10.1002/bies.202400006">https://doi.org/10.1002/bies.202400006</a>
  chicago: Stockwell, Imogen, Jake Watson, and Ingo H. Greger. “Tuning Synaptic Strength
    by Regulation of AMPA Glutamate Receptor Localization.” <i>BioEssays</i>. Wiley,
    2024. <a href="https://doi.org/10.1002/bies.202400006">https://doi.org/10.1002/bies.202400006</a>.
  ieee: I. Stockwell, J. Watson, and I. H. Greger, “Tuning synaptic strength by regulation
    of AMPA glutamate receptor localization,” <i>BioEssays</i>, vol. 46, no. 7. Wiley,
    2024.
  ista: Stockwell I, Watson J, Greger IH. 2024. Tuning synaptic strength by regulation
    of AMPA glutamate receptor localization. BioEssays. 46(7), 2400006.
  mla: Stockwell, Imogen, et al. “Tuning Synaptic Strength by Regulation of AMPA Glutamate
    Receptor Localization.” <i>BioEssays</i>, vol. 46, no. 7, 2400006, Wiley, 2024,
    doi:<a href="https://doi.org/10.1002/bies.202400006">10.1002/bies.202400006</a>.
  short: I. Stockwell, J. Watson, I.H. Greger, BioEssays 46 (2024).
date_created: 2024-05-12T22:01:02Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-08T07:25:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/bies.202400006
external_id:
  isi:
  - '001214545700001'
  pmid:
  - '38693811'
file:
- access_level: open_access
  checksum: dc8be74156657e8aab12a9d613233ee3
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-09T09:31:05Z
  date_updated: 2025-01-09T09:31:05Z
  file_id: '18801'
  file_name: 2024_BioEssays_Stockwell.pdf
  file_size: 775825
  relation: main_file
  success: 1
file_date_updated: 2025-01-09T09:31:05Z
fulldoi: https://doi.org/10.1002/bies.202400006
has_accepted_license: '1'
intvolume: '        46'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: BioEssays
publication_identifier:
  eissn:
  - 1521-1878
  issn:
  - 0265-9247
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning synaptic strength by regulation of AMPA glutamate receptor localization
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: 46
year: '2024'
...
---
_id: '17042'
abstract:
- lang: eng
  text: 'Bacterial cell walls are gigadalton-large cross-linked polymers with a wide
    range of motional amplitudes, including rather rigid as well as highly flexible
    parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information
    about intact cell walls. Here we investigate sensitivity and information content
    of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation
    experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased
    signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass
    sensitivity. The increased sensitivity allowed to obtain high-resolution spectra
    even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H
    MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints
    for choosing experiments to extract atomic-level details on cell-wall samples. '
article_processing_charge: No
author:
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
citation:
  ama: 'Schanda P. Raw data to “MAS NMR experiments of corynebacterial cell walls:
    complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” 2024.
    doi:<a href="https://doi.org/10.15479/AT:ISTA:17042">10.15479/AT:ISTA:17042</a>'
  apa: 'Schanda, P. (2024). Raw data to “MAS NMR experiments of corynebacterial cell
    walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.”
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:17042">https://doi.org/10.15479/AT:ISTA:17042</a>'
  chicago: 'Schanda, Paul. “Raw Data to ‘MAS NMR Experiments of Corynebacterial Cell
    Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.’”
    Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/AT:ISTA:17042">https://doi.org/10.15479/AT:ISTA:17042</a>.'
  ieee: 'P. Schanda, “Raw data to ‘MAS NMR experiments of corynebacterial cell walls:
    complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.’” Institute
    of Science and Technology Austria, 2024.'
  ista: 'Schanda P. 2024. Raw data to ‘MAS NMR experiments of corynebacterial cell
    walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments’,
    Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:17042">10.15479/AT:ISTA:17042</a>.'
  mla: 'Schanda, Paul. <i>Raw Data to “MAS NMR Experiments of Corynebacterial Cell
    Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.”</i>
    Institute of Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/AT:ISTA:17042">10.15479/AT:ISTA:17042</a>.'
  short: P. Schanda, (2024).
contributor:
- contributor_type: data_collector
  first_name: Alicia
  last_name: Vallet
- contributor_type: data_collector
  first_name: 'Isabel '
  last_name: Ayala
- contributor_type: data_collector
  first_name: Barbara
  last_name: Perrone
- contributor_type: data_collector
  first_name: Alia
  last_name: Hassan
- contributor_type: data_collector
  first_name: Catherine
  last_name: Bougault
corr_author: '1'
date_created: 2024-05-22T12:04:54Z
date_published: 2024-05-22T00:00:00Z
date_updated: 2025-09-09T12:01:41Z
day: '22'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.15479/AT:ISTA:17042
file:
- access_level: open_access
  checksum: eb55f0988342d927702353b75e07edfa
  content_type: text/plain
  creator: pschanda
  date_created: 2024-05-22T12:05:13Z
  date_updated: 2024-05-22T12:05:13Z
  file_id: '17043'
  file_name: Read_me.txt
  file_size: 2132
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 3393592acaf5ee1e032052c236780914
  content_type: application/zip
  creator: pschanda
  date_created: 2024-05-22T12:17:10Z
  date_updated: 2024-05-22T12:17:10Z
  file_id: '17044'
  file_name: raw_data_CryoMAS_cyronebacteria.zip
  file_size: 755704888
  relation: main_file
  success: 1
file_date_updated: 2024-05-22T12:17:10Z
fulldoi: https://doi.org/10.15479/AT:ISTA:17042
has_accepted_license: '1'
keyword:
- nuclear magnetic resonance
- NMR
- cellwall
- structural biology
- spectroscopy
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '17291'
    relation: used_in_publication
    status: public
status: public
title: 'Raw data to "MAS NMR experiments of corynebacterial cell walls: complementary
  1H- and CPMAS CryoProbe-enhanced 13C-detected experiments"'
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '17122'
abstract:
- lang: eng
  text: "Background: Motor alterations and lowered physical activity are common in
    affective disorders. Previous research has indicated a link between depressive
    symptoms and declining muscle strength primarily focusing on the elderly but not
    younger individuals. Thus, we aimed to evaluate the relationship between mood
    and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients
    (18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and
    schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy.
    The study was carried out as a prospective observational study at a German psychiatric
    university hospital between September 2021 and March 2022.\r\nMethods: Employing
    a standardized strength circuit consisting of computerized strength training devices,
    we measured the maximal muscle strength (Fmax) using three repetitions maximum
    across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3)
    over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood
    lipid profiling in a clinical setting. For analysis of psychopharmacotherapy,
    medication was split into activating (AM) and inhibiting (IM) medication and dosages
    were normalized by the respective WHO defined daily dose.\r\nResults: While we
    observed a significant decrease of the MADRS score and increase of the relative
    total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001),
    we did not reveal a significant bivariate correlation between disease severity
    (MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with
    longer disease history displayed reduced rTFmax (p = .048). IM was significantly
    associated with decreased rTFmax (p = .032). Regression models provide a more
    substantial effect of gender, age, and IM on muscle strength than the depressive
    episode itself (p < .001).\r\nConclusions: The results of the study indicate that
    disease severity and muscle strength are not associated in young to middle-aged
    inpatients with affective disorders using a strength circuit as observational
    measurement. Future research will be needed to differentiate the effect of medication,
    gender, and age on muscle strength and to develop interventions for prevention
    of muscle weakness, especially in younger patients with chronic affective illnesses."
acknowledgement: "This work was supported by the project ‘Fellows Ride’ of the Thomas
  Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’
  (to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL."
article_number: '401'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hannah
  full_name: Ramming, Hannah
  last_name: Ramming
- first_name: Linda
  full_name: Theuerkauf, Linda
  last_name: Theuerkauf
- first_name: Olaf
  full_name: Hoos, Olaf
  last_name: Hoos
- first_name: Katharina
  full_name: Lichter, Katharina
  id: 39302e62-fcfc-11ec-8196-8b01447dbd3d
  last_name: Lichter
  orcid: 0000-0002-1485-0351
- first_name: Sarah
  full_name: Kittel-Schneider, Sarah
  last_name: Kittel-Schneider
citation:
  ama: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association
    between maximal muscle strength, disease severity and psychopharmacotherapy among
    young to middle-aged inpatients with affective disorders – a prospective pilot
    study. <i>BMC Psychiatry</i>. 2024;24. doi:<a href="https://doi.org/10.1186/s12888-024-05849-2">10.1186/s12888-024-05849-2</a>
  apa: Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., &#38; Kittel-Schneider,
    S. (2024). The association between maximal muscle strength, disease severity and
    psychopharmacotherapy among young to middle-aged inpatients with affective disorders
    – a prospective pilot study. <i>BMC Psychiatry</i>. Springer Nature. <a href="https://doi.org/10.1186/s12888-024-05849-2">https://doi.org/10.1186/s12888-024-05849-2</a>
  chicago: Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah
    Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity
    and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective
    Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>. Springer Nature,
    2024. <a href="https://doi.org/10.1186/s12888-024-05849-2">https://doi.org/10.1186/s12888-024-05849-2</a>.
  ieee: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The
    association between maximal muscle strength, disease severity and psychopharmacotherapy
    among young to middle-aged inpatients with affective disorders – a prospective
    pilot study,” <i>BMC Psychiatry</i>, vol. 24. Springer Nature, 2024.
  ista: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The
    association between maximal muscle strength, disease severity and psychopharmacotherapy
    among young to middle-aged inpatients with affective disorders – a prospective
    pilot study. BMC Psychiatry. 24, 401.
  mla: Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease
    Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with
    Affective Disorders – a Prospective Pilot Study.” <i>BMC Psychiatry</i>, vol.
    24, 401, Springer Nature, 2024, doi:<a href="https://doi.org/10.1186/s12888-024-05849-2">10.1186/s12888-024-05849-2</a>.
  short: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC
    Psychiatry 24 (2024).
date_created: 2024-06-09T22:01:01Z
date_published: 2024-05-29T00:00:00Z
date_updated: 2025-04-23T07:51:51Z
day: '29'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1186/s12888-024-05849-2
external_id:
  pmid:
  - '38811916'
file:
- access_level: open_access
  checksum: 5df60d3c9388955c5b682ea34748d59d
  content_type: application/pdf
  creator: dernst
  date_created: 2024-06-10T10:44:26Z
  date_updated: 2024-06-10T10:44:26Z
  file_id: '17131'
  file_name: 2024_BMCPsychiatry_Ramming.pdf
  file_size: 2320147
  relation: main_file
  success: 1
file_date_updated: 2024-06-10T10:44:26Z
fulldoi: https://doi.org/10.1186/s12888-024-05849-2
has_accepted_license: '1'
intvolume: '        24'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Psychiatry
publication_identifier:
  eissn:
  - 1471-244X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The association between maximal muscle strength, disease severity and psychopharmacotherapy
  among young to middle-aged inpatients with affective disorders – a prospective pilot
  study
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: 24
year: '2024'
...
---
_id: '17139'
article_processing_charge: No
author:
- first_name: Alois
  full_name: Schlögl, Alois
  id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
  last_name: Schlögl
  orcid: 0000-0002-5621-8100
- first_name: Waleed
  full_name: Khalid, Waleed
  id: 097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1
  last_name: Khalid
- first_name: Stefano
  full_name: Elefante, Stefano
  id: 490F40CE-F248-11E8-B48F-1D18A9856A87
  last_name: Elefante
- first_name: Stephan
  full_name: Stadlbauer, Stephan
  id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
  last_name: Stadlbauer
citation:
  ama: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core
    is requested? In: <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>. EuroCC
    Austria; 2024:46. doi:<a href="https://doi.org/10.25365/phaidra.463">10.25365/phaidra.463</a>'
  apa: 'Schlögl, A., Khalid, W., Elefante, S., &#38; Stadlbauer, S. (2024). How much
    memory per CPU core is requested? In <i>ASHPC24 - Austrian-Slovenian HPC Meeting
    2024</i> (p. 46). Grundlsee, Austria: EuroCC Austria. <a href="https://doi.org/10.25365/phaidra.463">https://doi.org/10.25365/phaidra.463</a>'
  chicago: Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer.
    “How Much Memory per CPU Core Is Requested?” In <i>ASHPC24 - Austrian-Slovenian
    HPC Meeting 2024</i>, 46. EuroCC Austria, 2024. <a href="https://doi.org/10.25365/phaidra.463">https://doi.org/10.25365/phaidra.463</a>.
  ieee: A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per
    CPU core is requested?,” in <i>ASHPC24 - Austrian-Slovenian HPC Meeting 2024</i>,
    Grundlsee, Austria, 2024, p. 46.
  ista: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per
    CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian
    HPC Meeting, 46.'
  mla: Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” <i>ASHPC24
    - Austrian-Slovenian HPC Meeting 2024</i>, EuroCC Austria, 2024, p. 46, doi:<a
    href="https://doi.org/10.25365/phaidra.463">10.25365/phaidra.463</a>.
  short: A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian
    HPC Meeting 2024, EuroCC Austria, 2024, p. 46.
conference:
  end_date: 2024-06-13
  location: Grundlsee, Austria
  name: 'ASHPC: Austrian-Slovenian HPC Meeting'
  start_date: 2024-06-10
date_created: 2024-06-14T09:06:36Z
date_published: 2024-06-13T00:00:00Z
date_updated: 2024-06-17T09:40:37Z
day: '13'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.25365/phaidra.463
file:
- access_level: open_access
  checksum: f7d3dded6df2dcdb4818904cf2e1c183
  content_type: application/pdf
  creator: dernst
  date_created: 2024-06-17T09:36:51Z
  date_updated: 2024-06-17T09:36:51Z
  file_id: '17153'
  file_name: 2024_ASHPC_Schloegl.pdf
  file_size: 206746
  relation: main_file
  success: 1
file_date_updated: 2024-06-17T09:36:51Z
fulldoi: https://doi.org/10.25365/phaidra.463
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '46'
publication: ASHPC24 - Austrian-Slovenian HPC Meeting 2024
publication_identifier:
  isbn:
  - '9783200096455'
publication_status: published
publisher: EuroCC Austria
quality_controlled: '1'
status: public
title: How much memory per CPU core is requested?
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
fulldoi: https://doi.org/10.1002/advs.202408416
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
_id: '18579'
abstract:
- lang: eng
  text: 'Electrophysiological, calcium two-photon recordings and behavioral data for
    Vega-Zuniga et al.  Relevant information can be found in the ''README.txt'' files. '
acknowledged_ssus:
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: Bio
- _id: LifeSc
acknowledgement: Freyja Lange, Michael Schunn, and Todor Asenov
article_processing_charge: No
author:
- first_name: Tomas A
  full_name: Vega Zuniga, Tomas A
  id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
  last_name: Vega Zuniga
- first_name: Anton L
  full_name: Sumser, Anton L
  id: 3320A096-F248-11E8-B48F-1D18A9856A87
  last_name: Sumser
  orcid: 0000-0002-4792-1881
- first_name: Olga
  full_name: Symonova, Olga
  id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
  last_name: Symonova
  orcid: 0000-0003-2012-9947
- first_name: Peter
  full_name: Koppensteiner, Peter
  id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
  last_name: Koppensteiner
  orcid: 0000-0002-3509-1948
- first_name: Florian
  full_name: Schmidt, Florian
  id: A2EF226A-AF19-11E9-924C-0525E6697425
  last_name: Schmidt
- first_name: Maximilian A
  full_name: Jösch, Maximilian A
  id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
  last_name: Jösch
  orcid: 0000-0002-3937-1330
citation:
  ama: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA.
    A thalamic hub-and-spoke network enables visual perception during action by coordinating
    visuomotor dynamics. 2024. doi:<a href="https://doi.org/10.15479/AT:ISTA:18579">10.15479/AT:ISTA:18579</a>
  apa: Vega Zuniga, T. A., Sumser, A. L., Symonova, O., Koppensteiner, P., Schmidt,
    F., &#38; Jösch, M. A. (2024). A thalamic hub-and-spoke network enables visual
    perception during action by coordinating visuomotor dynamics. Institute of Science
    and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:18579">https://doi.org/10.15479/AT:ISTA:18579</a>
  chicago: Vega Zuniga, Tomas A, Anton L Sumser, Olga Symonova, Peter Koppensteiner,
    Florian Schmidt, and Maximilian A Jösch. “A Thalamic Hub-and-Spoke Network Enables
    Visual Perception during Action by Coordinating Visuomotor Dynamics.” Institute
    of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/AT:ISTA:18579">https://doi.org/10.15479/AT:ISTA:18579</a>.
  ieee: T. A. Vega Zuniga, A. L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt,
    and M. A. Jösch, “A thalamic hub-and-spoke network enables visual perception during
    action by coordinating visuomotor dynamics.” Institute of Science and Technology
    Austria, 2024.
  ista: Vega Zuniga TA, Sumser AL, Symonova O, Koppensteiner P, Schmidt F, Jösch MA.
    2024. A thalamic hub-and-spoke network enables visual perception during action
    by coordinating visuomotor dynamics, Institute of Science and Technology Austria,
    <a href="https://doi.org/10.15479/AT:ISTA:18579">10.15479/AT:ISTA:18579</a>.
  mla: Vega Zuniga, Tomas A., et al. <i>A Thalamic Hub-and-Spoke Network Enables Visual
    Perception during Action by Coordinating Visuomotor Dynamics</i>. Institute of
    Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/AT:ISTA:18579">10.15479/AT:ISTA:18579</a>.
  short: T.A. Vega Zuniga, A.L. Sumser, O. Symonova, P. Koppensteiner, F. Schmidt,
    M.A. Jösch, (2024).
corr_author: '1'
date_created: 2024-11-22T13:48:12Z
date_published: 2024-12-09T00:00:00Z
date_updated: 2026-06-18T18:12:08Z
day: '09'
ddc:
- '570'
department:
- _id: MaJö
doi: 10.15479/AT:ISTA:18579
ec_funded: 1
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fulldoi: https://doi.org/10.15479/AT:ISTA:18579
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month: '12'
oa: 1
oa_version: Published Version
project:
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  grant_number: ALTF 1098-2017
  name: Connecting sensory with motor processing in the superior colliculus
- _id: 266D407A-B435-11E9-9278-68D0E5697425
  grant_number: LT000256
  name: Neuronal networks of salience and spatial detection in the murine superior
    colliculus
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  call_identifier: H2020
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  name: Circuits of Visual Attention
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  grant_number: '101086580'
  name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses'
publisher: Institute of Science and Technology Austria
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status: public
title: A thalamic hub-and-spoke network enables visual perception during action by
  coordinating visuomotor dynamics
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: research_data
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---
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abstract:
- lang: eng
  text: "The evasive LWE assumption, proposed by Wee [Eurocrypt’22 Wee] for constructing
    a lattice-based optimal broadcast encryption, has shown to be a powerful assumption,
    adopted by subsequent works to construct advanced primitives ranging from ABE
    variants to obfuscation for null circuits. However, a closer look reveals significant
    differences among the precise assumption statements involved in different works,
    leading to the fundamental question of how these assumptions compare to each other.
    In this work, we initiate a more systematic study on evasive LWE assumptions:\r\n(i)
    Based on the standard LWE assumption, we construct simple counterexamples against
    three private-coin evasive LWE variants, used in [Crypto’22 Tsabary, Asiacrypt’22
    VWW, Crypto’23 ARYY] respectively, showing that these assumptions are unlikely
    to hold.\r\n\r\n(ii) Based on existing evasive LWE variants and our counterexamples,
    we propose and define three classes of plausible evasive LWE assumptions, suitably
    capturing all existing variants for which we are not aware of non-obfuscation-based
    counterexamples.\r\n\r\n(iii) We show that under our assumption formulations,
    the security proofs of [Asiacrypt’22 VWW] and [Crypto’23 ARYY] can be recovered,
    and we reason why the security proof of [Crypto’22 Tsabary] is also plausibly
    repairable using an appropriate evasive LWE assumption."
acknowledgement: The authors thank the anonymous reviewers for insightful comments
  which very much improved this work, in particular, sharing with us the counterexamples
  against a prior version of Hiding Evasive LWE, and against public-coin Evasive LWE
  when the sampler inputs B. Chris Brzuska and Ivy K. Y. Woo are supported by Research
  Council of Finland grant 358950. We thank Russell W. F. Lai and Hoeteck Wee for
  helpful discussions.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Chris
  full_name: Brzuska, Chris
  last_name: Brzuska
- first_name: Akin
  full_name: Ünal, Akin
  id: f6b56fb6-dc63-11ee-9dbf-f6780863a85a
  last_name: Ünal
  orcid: 0000-0002-8929-0221
- first_name: Ivy K.Y.
  full_name: Woo, Ivy K.Y.
  last_name: Woo
citation:
  ama: 'Brzuska C, Ünal A, Woo IKY. Evasive LWE assumptions: Definitions, classes,
    and counterexamples. In: <i>30th International Conference on the Theory and Application
    of Cryptology and Information Security</i>. Vol 15487. Springer Nature; 2024:418-449.
    doi:<a href="https://doi.org/10.1007/978-981-96-0894-2_14">10.1007/978-981-96-0894-2_14</a>'
  apa: 'Brzuska, C., Ünal, A., &#38; Woo, I. K. Y. (2024). Evasive LWE assumptions:
    Definitions, classes, and counterexamples. In <i>30th International Conference
    on the Theory and Application of Cryptology and Information Security</i> (Vol.
    15487, pp. 418–449). Kolkata, India: Springer Nature. <a href="https://doi.org/10.1007/978-981-96-0894-2_14">https://doi.org/10.1007/978-981-96-0894-2_14</a>'
  chicago: 'Brzuska, Chris, Akin Ünal, and Ivy K.Y. Woo. “Evasive LWE Assumptions:
    Definitions, Classes, and Counterexamples.” In <i>30th International Conference
    on the Theory and Application of Cryptology and Information Security</i>, 15487:418–49.
    Springer Nature, 2024. <a href="https://doi.org/10.1007/978-981-96-0894-2_14">https://doi.org/10.1007/978-981-96-0894-2_14</a>.'
  ieee: 'C. Brzuska, A. Ünal, and I. K. Y. Woo, “Evasive LWE assumptions: Definitions,
    classes, and counterexamples,” in <i>30th International Conference on the Theory
    and Application of Cryptology and Information Security</i>, Kolkata, India, 2024,
    vol. 15487, pp. 418–449.'
  ista: 'Brzuska C, Ünal A, Woo IKY. 2024. Evasive LWE assumptions: Definitions, classes,
    and counterexamples. 30th International Conference on the Theory and Application
    of Cryptology and Information Security. ASIACRYPT: Conference on the Theory and
    Application of Cryptology and Information Security, LNCS, vol. 15487, 418–449.'
  mla: 'Brzuska, Chris, et al. “Evasive LWE Assumptions: Definitions, Classes, and Counterexamples.”
    <i>30th International Conference on the Theory and Application of Cryptology and
    Information Security</i>, vol. 15487, Springer Nature, 2024, pp. 418–49, doi:<a
    href="https://doi.org/10.1007/978-981-96-0894-2_14">10.1007/978-981-96-0894-2_14</a>.'
  short: C. Brzuska, A. Ünal, I.K.Y. Woo, in:, 30th International Conference on the
    Theory and Application of Cryptology and Information Security, Springer Nature,
    2024, pp. 418–449.
conference:
  end_date: 2024-12-13
  location: Kolkata, India
  name: 'ASIACRYPT: Conference on the Theory and Application of Cryptology and Information
    Security'
  start_date: 2024-12-09
date_created: 2025-01-05T23:01:56Z
date_published: 2024-12-13T00:00:00Z
date_updated: 2025-09-09T12:00:51Z
day: '13'
department:
- _id: KrPi
doi: 10.1007/978-981-96-0894-2_14
external_id:
  isi:
  - '001443890800014'
fulldoi: https://doi.org/10.1007/978-981-96-0894-2_14
intvolume: '     15487'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2024/2000
month: '12'
oa: 1
oa_version: Preprint
page: 418-449
publication: 30th International Conference on the Theory and Application of Cryptology
  and Information Security
publication_identifier:
  eissn:
  - 1611-3349
  isbn:
  - '9789819608935'
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Evasive LWE assumptions: Definitions, classes, and counterexamples'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15487
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18998'
abstract:
- lang: eng
  text: Word embeddings represent language vocabularies as clouds of d-dimensional
    points. We investigate how information is conveyed by the general shape of these
    clouds, instead of representing the semantic meaning of each token. Specifically,
    we use the notion of persistent homology from topological data analysis (TDA)
    to measure the distances between language pairs from the shape of their unlabeled
    embeddings. These distances quantify the degree of non-isometry of the embeddings.
    To distinguish whether these differences are random training errors or capture
    real information about the languages, we use the computed distance matrices to
    construct language phylogenetic trees over 81 Indo-European languages. Careful
    evaluation shows that our reconstructed trees exhibit strong and statistically-significant
    similarities to the reference.
article_processing_charge: No
arxiv: 1
author:
- first_name: Ondrej
  full_name: Draganov, Ondrej
  id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
  last_name: Draganov
  orcid: 0000-0003-0464-3823
- first_name: Steven
  full_name: Skiena, Steven
  last_name: Skiena
citation:
  ama: 'Draganov O, Skiena S. The shape of word embeddings: Quantifying non-isometry
    with topological data analysis. In: <i>Findings of the Association for Computational
    Linguistics: EMNLP 2024</i>. Association for Computational Linguistics; 2024:12080-12099.
    doi:<a href="https://doi.org/10.18653/v1/2024.findings-emnlp.705">10.18653/v1/2024.findings-emnlp.705</a>'
  apa: 'Draganov, O., &#38; Skiena, S. (2024). The shape of word embeddings: Quantifying
    non-isometry with topological data analysis. In <i>Findings of the Association
    for Computational Linguistics: EMNLP 2024</i> (pp. 12080–12099). Miami, FL, United
    States: Association for Computational Linguistics. <a href="https://doi.org/10.18653/v1/2024.findings-emnlp.705">https://doi.org/10.18653/v1/2024.findings-emnlp.705</a>'
  chicago: 'Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying
    Non-Isometry with Topological Data Analysis.” In <i>Findings of the Association
    for Computational Linguistics: EMNLP 2024</i>, 12080–99. Association for Computational
    Linguistics, 2024. <a href="https://doi.org/10.18653/v1/2024.findings-emnlp.705">https://doi.org/10.18653/v1/2024.findings-emnlp.705</a>.'
  ieee: 'O. Draganov and S. Skiena, “The shape of word embeddings: Quantifying non-isometry
    with topological data analysis,” in <i>Findings of the Association for Computational
    Linguistics: EMNLP 2024</i>, Miami, FL, United States, 2024, pp. 12080–12099.'
  ista: 'Draganov O, Skiena S. 2024. The shape of word embeddings: Quantifying non-isometry
    with topological data analysis. Findings of the Association for Computational
    Linguistics: EMNLP 2024. EMNLP: Conference on Empirical Methods in Natural Language
    Processing, 12080–12099.'
  mla: 'Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying
    Non-Isometry with Topological Data Analysis.” <i>Findings of the Association for
    Computational Linguistics: EMNLP 2024</i>, Association for Computational Linguistics,
    2024, pp. 12080–99, doi:<a href="https://doi.org/10.18653/v1/2024.findings-emnlp.705">10.18653/v1/2024.findings-emnlp.705</a>.'
  short: 'O. Draganov, S. Skiena, in:, Findings of the Association for Computational
    Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp.
    12080–12099.'
conference:
  end_date: 2024-11-16
  location: Miami, FL, United States
  name: 'EMNLP: Conference on Empirical Methods in Natural Language Processing'
  start_date: 2024-11-12
corr_author: '1'
date_created: 2025-02-04T16:19:28Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-02-10T08:21:37Z
day: '01'
ddc:
- '500'
department:
- _id: GradSch
- _id: HeEd
doi: 10.18653/v1/2024.findings-emnlp.705
external_id:
  arxiv:
  - '2404.00500'
file:
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  creator: dernst
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  date_updated: 2025-02-10T08:20:34Z
  file_id: '19016'
  file_name: 2024_EMNLP_Draganov.pdf
  file_size: 1312638
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  success: 1
file_date_updated: 2025-02-10T08:20:34Z
fulldoi: https://doi.org/10.18653/v1/2024.findings-emnlp.705
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 12080-12099
publication: 'Findings of the Association for Computational Linguistics: EMNLP 2024'
publication_status: published
publisher: Association for Computational Linguistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The shape of word embeddings: Quantifying non-isometry with topological data
  analysis'
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
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18999'
abstract:
- lang: eng
  text: Exploring the shape of point configurations has been a key driver in the evolution
    of TDA (short for topological data analysis) since its infancy. This survey illustrates
    the recent efforts to broaden these ideas to model spatial interactions among
    multiple configurations, each distinguished by a color. It describes advances
    in this area and prepares the ground for further exploration by mentioning unresolved
    questions and promising research avenues while focusing on the overlap with discrete
    geometry.
article_number: '2406.04102'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastiano
  full_name: Cultrera di Montesano, Sebastiano
  id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
  last_name: Cultrera di Montesano
  orcid: 0000-0001-6249-0832
- first_name: Ondrej
  full_name: Draganov, Ondrej
  id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
  last_name: Draganov
  orcid: 0000-0003-0464-3823
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Morteza
  full_name: Saghafian, Morteza
  id: f86f7148-b140-11ec-9577-95435b8df824
  last_name: Saghafian
citation:
  ama: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
    topological data analysis. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/ARXIV.2406.04102">10.48550/ARXIV.2406.04102</a>
  apa: Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian,
    M. (n.d.). Chromatic topological data analysis. <i>arXiv</i>. <a href="https://doi.org/10.48550/ARXIV.2406.04102">https://doi.org/10.48550/ARXIV.2406.04102</a>
  chicago: Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner,
    and Morteza Saghafian. “Chromatic Topological Data Analysis.” <i>ArXiv</i>, n.d.
    <a href="https://doi.org/10.48550/ARXIV.2406.04102">https://doi.org/10.48550/ARXIV.2406.04102</a>.
  ieee: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian,
    “Chromatic topological data analysis,” <i>arXiv</i>. .
  ista: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
    topological data analysis. arXiv, 2406.04102.
  mla: Cultrera di Montesano, Sebastiano, et al. “Chromatic Topological Data Analysis.”
    <i>ArXiv</i>, 2406.04102, doi:<a href="https://doi.org/10.48550/ARXIV.2406.04102">10.48550/ARXIV.2406.04102</a>.
  short: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv
    (n.d.).
corr_author: '1'
date_created: 2025-02-04T16:21:21Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2025-02-10T08:14:27Z
day: '06'
ddc:
- '510'
department:
- _id: GradSch
- _id: HeEd
doi: 10.48550/ARXIV.2406.04102
external_id:
  arxiv:
  - '2406.04102'
fulldoi: https://doi.org/10.48550/ARXIV.2406.04102
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2406.04102
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Chromatic topological data analysis
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...