---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21746'
abstract:
- lang: eng
text: As vertebrates transitioned from water to land, locomotion shifted from undulatory
swimming to limb-based movement. How spinal circuits and their cell types evolved
to support this transition remains unclear. We leverage frog metamorphosis, which
recapitulates this transition within a single organism, to define how spinal circuits
generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture
is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons.
As limbs develop and their movement complexifies, spinal circuits expand in neuron
number and subtype diversity. This expansion is most pronounced for V1 inhibitory
neurons, which increase ∼70-fold and diversify into transcriptionally distinct
subtypes. Disrupting transcription factors defining emerging motor and V1 populations
reveals molecular segregation between swim and limb circuits, highlighting the
role of subtype diversity in motor coordination. A multifold increase in inhibitory
neuron diversity thus underlies the tail-to-limb locomotor transition, providing
a framework for spinal circuit adaptation during vertebrate evolution.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We would like to thank the members of the Sweeney Lab, Mario de
Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript.
We are also grateful to Tom Jessell and Chris Kintner for their scientific insight
and mentorship during the conception of this project. It would also have not been
possible without the technical support of the Aquatics and Imaging and Optics Facility
support teams (ISTA). We thank Martin Estermann for preparing the initial draft
of the graphical abstract and Niki Barolini for the final version. In addition,
we thank our funding sources for providing the resources to do these experiments:
GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon
Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special
Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.),
Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858
(to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH
grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC)
(to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472
(to Z.H.), and Project A.L.S. (to S.B.-M.).'
article_number: '117227'
article_processing_charge: Yes
article_type: original
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
- first_name: 'Florina Alexandra '
full_name: 'Toma, Florina Alexandra '
id: 2f73f876-f128-11eb-9611-b96b5a30cb0e
last_name: Toma
- first_name: Y
full_name: Ignatyev, Y
last_name: Ignatyev
- first_name: Zoe P
full_name: Harrington, Zoe P
id: a8144562-32c9-11ee-b5ce-d9800628bda2
last_name: Harrington
orcid: 0009-0008-0158-4032
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matthijs Geert
full_name: Smits, Matthijs Geert
id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0
last_name: Smits
- first_name: Marco
full_name: Dalla Vecchia, Marco
id: 02a7a869-ff06-11ed-a87f-86649d6077e5
last_name: Dalla Vecchia
- first_name: Alexandra J.
full_name: Trevisan, Alexandra J.
last_name: Trevisan
- first_name: Phillip
full_name: Chapman, Phillip
last_name: Chapman
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227
apa: Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M.,
Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2026.117227
chicago: Vijatovic, David, Florina Alexandra Toma, Y Ignatyev, Zoe P Harrington,
Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold
Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell
Reports. Elsevier, 2026. https://doi.org/10.1016/j.celrep.2026.117227.
ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell
types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Elsevier,
2026.
ista: Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits
MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto
MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 45(4), 117227.
mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types
with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227,
Elsevier, 2026, doi:10.1016/j.celrep.2026.117227.
short: D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild,
M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton,
M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).
corr_author: '1'
date_created: 2026-04-19T22:07:43Z
date_published: 2026-04-28T00:00:00Z
date_updated: 2026-05-04T12:27:06Z
day: '28'
ddc:
- '570'
department:
- _id: LoSw
- _id: GradSch
- _id: TiVo
- _id: Bio
- _id: NiBa
doi: 10.1016/j.celrep.2026.117227
external_id:
pmid:
- '41964955 '
file:
- access_level: open_access
checksum: 0d26cdb5b8d8dec3a911d8261a65cdef
content_type: application/pdf
creator: dernst
date_created: 2026-05-04T12:20:10Z
date_updated: 2026-05-04T12:20:10Z
file_id: '21795'
file_name: 2026_CellReports_Vijatovic.pdf
file_size: 14925958
relation: main_file
success: 1
file_date_updated: 2026-05-04T12:20:10Z
has_accepted_license: '1'
intvolume: ' 45'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e
grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
- _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473
grant_number: CZI01
name: Tools for automation and feedback microscopy
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multifold increase in spinal inhibitory cell types with emergence of limb movement
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: 45
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21895'
abstract:
- lang: eng
text: The mammalian brain organises knowledge about entities in the world and relationships
between them using cognitive maps. When forming a cognitive map, there is a necessary
trade-off between extending the map to make novel inferences, and storing a veridical
copy of past experience. However, the neural mechanisms that control this trade-off
remain unknown. Using a cross-scale approach that combines a pharmacological intervention
in humans with neural network modelling, we show that the neuromodulator noradrenaline
elicits a significant ‘spread of association’ across hippocampal cognitive maps.
This neural spread of association can be explained by changes in synaptic plasticity
that predict overgeneralisation in behaviour. Thus, elevated noradrenaline during
learning increases the ‘smoothing kernel’ for plasticity across the cognitive
map, allowing disparate memories to become linked and distorted.
acknowledgement: 'We would like to thank Chamith Halahakoon, Phil Cowen, Angharad
De Cates, Beata Godlewska, Riccardo De Giorgi, Katherine Smith and Edoardo Ostinelli
for enabling this study by providing medical cover. We would like to thank Douglas
F. Tomé and Everton J. Agnes for their guidance and advice with earlier versions
of the neural network model. We would like to thank Rob Froemke for helpful discussion
when preparing the experiments. We thank Leonie Glitz and Valentina Mancini for
comments on an earlier version of the manuscript. R.S.K. was supported by an EPSRC/MRC-funded
studentship (EP/L016052/1). P.P. was supported by the Cambridge Trust, Trinity Henry
Barlow Scholarship and Trinity Hall Brockhouse Scholarship. L.C. is supported by
the Foundation for Science and Technology (FCT) (Portuguese State Budget: UID/PSI/01662/2020;
Research fellowship: 2021.00415.CEECIND). W.T.C. is funded by the Wellcome Trust
[225924/Z/22/Z]. H.C.B. is supported by a UKRI Future Leaders Fellowship (MR/W008939/1)
and the Wellcome Institutional Strategic Support Fund. H.C.B. and J.X.O. are supported
by the Medical Research Council (MR/W01971X/1). The study was supported by the NIHR
Oxford Health Biomedical Research Centre (NIHR203316). The views expressed are those
of the author(s) and not necessarily those of the NIHR or the Department of Health
and Social Care. The Wellcome Centre for Integrative Neuroimaging is supported by
core funding from the Wellcome Trust (203139/Z/16/Z and 203139/A/16/Z). This research
was funded in part by the Wellcome Trust. For the purpose of open access, the author(s)
have applied a CC BY public copyright license to any Author Accepted Manuscript
version arising from this submission.'
article_number: '3961'
article_processing_charge: Yes
article_type: original
author:
- first_name: Renée S.
full_name: Koolschijn, Renée S.
last_name: Koolschijn
- first_name: Prakriti
full_name: Parthasarathy, Prakriti
last_name: Parthasarathy
- first_name: Michael
full_name: Browning, Michael
last_name: Browning
- first_name: Xenia
full_name: Przygodda, Xenia
last_name: Przygodda
- first_name: Liliana P.
full_name: Capitão, Liliana P.
last_name: Capitão
- first_name: William T.
full_name: Clarke, William T.
last_name: Clarke
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Jill X.
full_name: O’Reilly, Jill X.
last_name: O’Reilly
- first_name: Helen C.
full_name: Barron, Helen C.
last_name: Barron
citation:
ama: Koolschijn RS, Parthasarathy P, Browning M, et al. Noradrenaline causes a spread
of association in the hippocampal cognitive map. Nature Communications.
2026;17. doi:10.1038/s41467-026-70659-x
apa: Koolschijn, R. S., Parthasarathy, P., Browning, M., Przygodda, X., Capitão,
L. P., Clarke, W. T., … Barron, H. C. (2026). Noradrenaline causes a spread of
association in the hippocampal cognitive map. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-026-70659-x
chicago: Koolschijn, Renée S., Prakriti Parthasarathy, Michael Browning, Xenia Przygodda,
Liliana P. Capitão, William T. Clarke, Tim P Vogels, Jill X. O’Reilly, and Helen
C. Barron. “Noradrenaline Causes a Spread of Association in the Hippocampal Cognitive
Map.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-70659-x.
ieee: R. S. Koolschijn et al., “Noradrenaline causes a spread of association
in the hippocampal cognitive map,” Nature Communications, vol. 17. Springer
Nature, 2026.
ista: Koolschijn RS, Parthasarathy P, Browning M, Przygodda X, Capitão LP, Clarke
WT, Vogels TP, O’Reilly JX, Barron HC. 2026. Noradrenaline causes a spread of
association in the hippocampal cognitive map. Nature Communications. 17, 3961.
mla: Koolschijn, Renée S., et al. “Noradrenaline Causes a Spread of Association
in the Hippocampal Cognitive Map.” Nature Communications, vol. 17, 3961,
Springer Nature, 2026, doi:10.1038/s41467-026-70659-x.
short: R.S. Koolschijn, P. Parthasarathy, M. Browning, X. Przygodda, L.P. Capitão,
W.T. Clarke, T.P. Vogels, J.X. O’Reilly, H.C. Barron, Nature Communications 17
(2026).
date_created: 2026-05-20T14:30:37Z
date_published: 2026-05-01T00:00:00Z
date_updated: 2026-05-21T07:05:01Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1038/s41467-026-70659-x
external_id:
pmid:
- '41832186'
file:
- access_level: open_access
checksum: 1b529e06b1c5d6e085d60743317fd4f9
content_type: application/pdf
creator: dernst
date_created: 2026-05-21T07:01:35Z
date_updated: 2026-05-21T07:01:35Z
file_id: '21905'
file_name: 2026_NatureComm_Koolschijn.pdf
file_size: 2059139
relation: main_file
success: 1
file_date_updated: 2026-05-21T07:01:35Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noradrenaline causes a spread of association in the hippocampal cognitive map
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: 17
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21378'
abstract:
- lang: eng
text: From insects to mammals, essential brain functions, such as forming long-term
memories (LTMs), increase metabolic activity in stimulated neurons to meet the
energetic demand associated with brain activation. However, while impairing neuronal
metabolism limits brain performance, whether expanding the metabolic capacity
of neurons boosts brain function remains poorly understood. Here, we show that
LTM formation of flies and mice can be enhanced by increasing mitochondrial metabolism
in central memory circuits. By knocking down the mitochondrial Ca2+ exporter Letm1,
we favour Ca2+ retention in the mitochondrial matrix of neurons due to reduction
of mitochondrial H+/Ca2+ exchange. The resulting increase in mitochondrial Ca2+
over-activates mitochondrial metabolism in neurons of central memory circuits,
leading to improved LTM storage in training paradigms in which wild-type counterparts
of both species fail to remember. Our findings unveil an evolutionarily conserved
mechanism that controls mitochondrial metabolism in neurons and indicate its involvement
in shaping higher brain functions, such as LTM.
acknowledgement: We thank all members of the laboratory of J.d.J.-S. for insightful
discussions and comments. We thank S. Perez for technical assistance. This work
was made possible by the Paris Brain Institute Diane Barriere Chair in Synaptic
Bioenergetics awarded to J.d.J.-S., who is also supported by an ERC Starting Grant
(SynaptoEnergy, European Research Council; ERC-StG-852873), 2019 ATIP-Avenir Grant
(CNRS, Inserm), a Big Brain Theory Grant (ICM Foundation) and a Kavli Exploratory
Award (Kavli Foundation). This work was also supported by an ERC Advanced Grant
(EnergyMeMo; ERC-AdG-741550) to T.P. and grants from the Agence Nationale de la
Recherche to P.Y.P. (ANR-20-CE92-0047-01), T.P. (ANR-23-CE16-0029-01), A.P. and
J.d.J.-S. (ANR-22-CE16-0020) and J.d.J.-S. (ANR-24-CE16-0221). T.P., P.Y.P. and
J.d.J.-S. are permanent CNRS researchers. A.P. is a permanent ESPCI associate professor.
T.C. was funded by the French Ministry of Research and the Fondation pour la Recherche
Médicale. V.R. was funded by the Max Planck Society, the Chan Zuckerberg Initiative
DAF, an advised fund of the Silicon Valley Community Foundation grant number 2024-349543
and the NIH Director’s New Innovator Award (DP2 MH140148). A.B.-G. and C.R.-D. received
funding from an ERC Starting Grant (HighMemory; ERC-StG-948217), the Ministry of
Economy and Competitiveness (PID2021-122795OB-I00) and the Departament d’Economia
i Coneixement de la Generalitat de Catalunya (SGR 00022). T.P.V. was funded by the
Wellcome Trust and a Royal Society Sir Henry Dale Research Fellowship (WT100000)
and a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z). K.G. was supported
by the DIM C-BRAINS, funded by the Conseil Régional d’Ile-de-France. The contributions
of H.F. and E.R.S. were supported by the Howard Hughes Medical Institute. The PHENO-ICMice
animal Core at ICM is supported by two ‘Investissements d’avenir’ (ANR-10- IAIHU-06
and ANR-11-INBS-0011-NeurATRIS) and the Fondation pour la Recherche Médicale.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Anjali
full_name: Amrapali Vishwanath, Anjali
last_name: Amrapali Vishwanath
- first_name: Typhaine
full_name: Comyn, Typhaine
last_name: Comyn
- first_name: Rodrigo G.
full_name: Mira, Rodrigo G.
last_name: Mira
- first_name: Claire
full_name: Brossier, Claire
last_name: Brossier
- first_name: Carlos
full_name: Pascual-Caro, Carlos
last_name: Pascual-Caro
- first_name: Maya
full_name: Faour, Maya
last_name: Faour
- first_name: Kahina
full_name: Boumendil, Kahina
last_name: Boumendil
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Carla
full_name: Ramon-Duaso, Carla
last_name: Ramon-Duaso
- first_name: Ruolin
full_name: Fan, Ruolin
last_name: Fan
- first_name: Kishalay
full_name: Ghosh, Kishalay
last_name: Ghosh
- first_name: Helen
full_name: Farrants, Helen
last_name: Farrants
- first_name: Jean-Paul
full_name: Berwick, Jean-Paul
last_name: Berwick
- first_name: Riya
full_name: Sivakumar, Riya
last_name: Sivakumar
- first_name: Mario
full_name: Lopez-Manzaneda, Mario
last_name: Lopez-Manzaneda
- first_name: Eric R.
full_name: Schreiter, Eric R.
last_name: Schreiter
- first_name: Thomas
full_name: Preat, Thomas
last_name: Preat
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Vidhya
full_name: Rangaraju, Vidhya
last_name: Rangaraju
- first_name: Arnau
full_name: Busquets-Garcia, Arnau
last_name: Busquets-Garcia
- first_name: Pierre-Yves
full_name: Plaçais, Pierre-Yves
last_name: Plaçais
- first_name: Alice
full_name: Pavlowsky, Alice
last_name: Pavlowsky
- first_name: Jaime
full_name: de Juan-Sanz, Jaime
last_name: de Juan-Sanz
citation:
ama: Amrapali Vishwanath A, Comyn T, Mira RG, et al. Mitochondrial Ca2+ efflux controls
neuronal metabolism and long-term memory across species. Nature Metabolism.
2026;8(2):467-488. doi:10.1038/s42255-026-01451-w
apa: Amrapali Vishwanath, A., Comyn, T., Mira, R. G., Brossier, C., Pascual-Caro,
C., Faour, M., … de Juan-Sanz, J. (2026). Mitochondrial Ca2+ efflux controls neuronal
metabolism and long-term memory across species. Nature Metabolism. Springer
Nature. https://doi.org/10.1038/s42255-026-01451-w
chicago: Amrapali Vishwanath, Anjali, Typhaine Comyn, Rodrigo G. Mira, Claire Brossier,
Carlos Pascual-Caro, Maya Faour, Kahina Boumendil, et al. “Mitochondrial Ca2+
Efflux Controls Neuronal Metabolism and Long-Term Memory across Species.” Nature
Metabolism. Springer Nature, 2026. https://doi.org/10.1038/s42255-026-01451-w.
ieee: A. Amrapali Vishwanath et al., “Mitochondrial Ca2+ efflux controls
neuronal metabolism and long-term memory across species,” Nature Metabolism,
vol. 8, no. 2. Springer Nature, pp. 467–488, 2026.
ista: Amrapali Vishwanath A, Comyn T, Mira RG, Brossier C, Pascual-Caro C, Faour
M, Boumendil K, Chintaluri C, Ramon-Duaso C, Fan R, Ghosh K, Farrants H, Berwick
J-P, Sivakumar R, Lopez-Manzaneda M, Schreiter ER, Preat T, Vogels TP, Rangaraju
V, Busquets-Garcia A, Plaçais P-Y, Pavlowsky A, de Juan-Sanz J. 2026. Mitochondrial
Ca2+ efflux controls neuronal metabolism and long-term memory across species.
Nature Metabolism. 8(2), 467–488.
mla: Amrapali Vishwanath, Anjali, et al. “Mitochondrial Ca2+ Efflux Controls Neuronal
Metabolism and Long-Term Memory across Species.” Nature Metabolism, vol.
8, no. 2, Springer Nature, 2026, pp. 467–88, doi:10.1038/s42255-026-01451-w.
short: A. Amrapali Vishwanath, T. Comyn, R.G. Mira, C. Brossier, C. Pascual-Caro,
M. Faour, K. Boumendil, C. Chintaluri, C. Ramon-Duaso, R. Fan, K. Ghosh, H. Farrants,
J.-P. Berwick, R. Sivakumar, M. Lopez-Manzaneda, E.R. Schreiter, T. Preat, T.P.
Vogels, V. Rangaraju, A. Busquets-Garcia, P.-Y. Plaçais, A. Pavlowsky, J. de Juan-Sanz,
Nature Metabolism 8 (2026) 467–488.
das_tickbox: '1'
date_created: 2026-03-02T10:04:49Z
date_published: 2026-02-11T00:00:00Z
date_updated: 2026-07-13T12:30:14Z
day: '11'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1038/s42255-026-01451-w
external_id:
pmid:
- '41673453'
file:
- access_level: open_access
checksum: 365932a599d05bc9ce8a57204e7a1465
content_type: application/pdf
creator: dernst
date_created: 2026-03-02T15:21:27Z
date_updated: 2026-03-02T15:21:27Z
file_id: '21392'
file_name: 2026_NatureMetab_AmrapaliVishwanath.pdf
file_size: 5326608
relation: main_file
success: 1
file_date_updated: 2026-03-02T15:21:27Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 467-488
pmid: 1
project:
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Nature Metabolism
publication_identifier:
eissn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mitochondrial Ca2+ efflux controls neuronal metabolism and long-term memory
across species
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: 8
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '22295'
abstract:
- lang: eng
text: 'Despite the functional diversity of over 100 causal genes1,2,3, phenotypic
convergence across models may reveal common neurobiological processes in autism
spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse
models of ASD using single-nucleus multi-omic sequencing across three developmental
stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked
mutations converged on perturbations of the radial glial cell lineage. These alterations
reflect a transient developmental delay rather than lasting lineage misspecification
and resolve by postnatal stages. Molecularly, the largest transcriptional differences
emerged in neurons at early postnatal stages. These changes included downregulation
of synaptic and ion channel-related genes, consistent with homeostatic adaptation
or delayed maturation. Network analysis showed molecular convergence across models
within each developmental stage, suggesting that diverse mutations linked to ASD
impinge on common, stage-specific processes. Convergence becomes less pronounced
by postnatal day 14, highlighting the dynamic nature of ASD-associated changes.
Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology
corroborated this pattern: mutants generally showed altered neuronal excitability
and synaptic properties with model-specific nuances. Our study also highlighted
sex-specific gene expression alterations, with female mice often displaying larger
effect sizes than male mice. Together, our findings provide a comprehensive view
of developmental cellular and molecular dynamics across models of ASD.'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical
assistance; A. Stichelberger and S. Liegenfeld for the management of our animal
colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance;
C. Jansen and the Scientific Computing Facility for bioinformatics support and technical
assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation
sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support
with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted
in Fig. 1; and all members of the laboratory of G.N. for their support and discussions.
This study was supported by the Scientific Service Units of ISTA through resources
provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk
RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities, member of the Vienna BioCenter. This work was supported by a European
Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by
the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. 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: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Sergey
full_name: Isaev, Sergey
last_name: Isaev
- first_name: Michela
full_name: Lisi, Michela
id: 39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c
last_name: Lisi
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Christoph
full_name: Büschl, Christoph
id: 2a8c054c-0913-11ee-9159-f8ef515809ed
last_name: Büschl
- first_name: Sabrina
full_name: Ladstätter, Sabrina
last_name: Ladstätter
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Matteo
full_name: Barel, Matteo
id: 8959927b-2236-11ed-bd6e-ea83d94ade0e
last_name: Barel
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Stephan
full_name: Reichl, Stephan
last_name: Reichl
- first_name: Gintarė
full_name: Sendžikaitė, Gintarė
id: dd6d52f2-c50d-11eb-9548-bcf0ff82b344
last_name: Sendžikaitė
- first_name: Satish
full_name: Arcot Jayaram, Satish
id: b0bbee33-09f7-11eb-909c-8b358058d28a
last_name: Arcot Jayaram
orcid: 0000-0002-2479-2669
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Peter Vasili
full_name: Kharchenko, Peter Vasili
id: 0095641e-7eb7-11f1-8665-aec51a2ab5e0
last_name: Kharchenko
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across
autism spectrum disorder mouse models. Nature. 2026. doi:10.1038/s41586-026-10679-1
apa: Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino,
G. (2026). Cortical development dynamics across autism spectrum disorder mouse
models. Nature. Springer Nature. https://doi.org/10.1038/s41586-026-10679-1
chicago: Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl,
Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across
Autism Spectrum Disorder Mouse Models.” Nature. Springer Nature, 2026.
https://doi.org/10.1038/s41586-026-10679-1.
ieee: L. A. Schwarz et al., “Cortical development dynamics across autism
spectrum disorder mouse models,” Nature. Springer Nature, 2026.
ista: Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira
B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl
S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche
J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics
across autism spectrum disorder mouse models. Nature.
mla: Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum
Disorder Mouse Models.” Nature, Springer Nature, 2026, doi:10.1038/s41586-026-10679-1.
short: L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter,
B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi,
T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M.
Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino,
Nature (2026).
corr_author: '1'
dataavailabilitystatement: Single-nucleus multiomics data are available from the Gene
Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment
(refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz).
Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz).
Source data are provided with this paper. Scripts and analyses that support the
main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).
date_created: 2026-07-13T09:47:21Z
date_published: 2026-06-17T00:00:00Z
date_updated: 2026-07-13T12:58:19Z
day: '17'
ddc:
- '570'
department:
- _id: AnKi
- _id: GaNo
- _id: TiVo
- _id: ScienComp
- _id: GradSch
- _id: Bio
- _id: PreCl
doi: 10.1038/s41586-026-10679-1
external_id:
pmid:
- '42310454'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-026-10679-1
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _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: 9B91375C-BA93-11EA-9121-9846C619BF3A
grant_number: '707964'
name: Critical windows and reversibility of ASD associated with mutations in chromatin
remodelers
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: ebb38b5d-77a9-11ec-83b8-a42e08120a88
grant_number: FG1803 49015
name: Neurobiology of anxiety in autism spectrum disorders
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Cortical development dynamics across autism spectrum disorder mouse models
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
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20986'
abstract:
- lang: eng
text: During complex vocal interactions, different features of acoustic stimuli
are integrated to produce appropriate vocal responses,1 such as copying sounds
during vocal matching behavior in some animals.2,3,4,5,6,7,8,9,10,11,12 However,
little is known about the interplay and possible trade-offs between the different
temporal and spectral acoustic features during these vocal exchanges.2,13,14 Nightingales
can flexibly match the pitch of their tonal “whistle songs” in real time during
counter-singing duels.15,16 Here, we show that the syllable duration of whistle
playbacks could alter the song responses of wild nightingales, causing their whistle
duration distribution to shift toward the presented stimulus duration. When exposed
to whistle playbacks featuring unnatural combinations of pitch and duration, nightingales
demonstrate a flexible trade-off between pitch matching and temporal imitation,
yet they are constrained by their vocal repertoire. They selectively adapted their
vocal responses to approximate these novel stimuli, aligning them with their natural
whistle repertoire. We developed a computational model of nightingale whistle-matching
behavior that revealed a hierarchical organization of acoustic feature production.
During whistle matching, the feature integration process is constrained by the
duration of syllables, and pitch matching follows within this temporal framework,
forcing a trade-off between the two features. Our findings reveal a complex interplay
between the spectral and temporal domains that shapes song-matching behavior.
acknowledgement: 'We would like to thank J. Benichov and N. Hein for their help with
fieldwork; M. Ramadas for helping with the segmentation analysis; T. Eliav, C. Chintaluri,
G. Tkacik, and A. Navas for providing helpful comments to the project and manuscript;
and A. Costalunga for the drawings of nightingales. Funding sources: The Joachim
Herz Stiftung Add-on Fellowships for Interdisciplinary Life Science, awarded to
G.C.; the ERC Consolidator Grant 819603 SYNAPSEEK, awarded to T.P.V.; and DFG Research
Unit 5768–532521431, DFG Research Grant-547921981, DFG SFB 1315–327654276, and the
ERC Starting Grant 757459 MIDNIGHT, awarded to D.V.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Juan Sebastian
full_name: Calderon Garcia, Juan Sebastian
id: 1271b54b-dbcd-11ea-9d1d-d92da838fe2c
last_name: Calderon Garcia
- first_name: Giacomo
full_name: Costalunga, Giacomo
last_name: Costalunga
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Daniela
full_name: Vallentin, Daniela
last_name: Vallentin
citation:
ama: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. Interplay between
syllable duration and pitch during whistle matching in wild nightingales. Current
Biology. 2026;36(3):791-798.e6. doi:10.1016/j.cub.2025.12.025
apa: Calderon Garcia, J. S., Costalunga, G., Vogels, T. P., & Vallentin, D.
(2026). Interplay between syllable duration and pitch during whistle matching
in wild nightingales. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2025.12.025
chicago: Calderon Garcia, Juan Sebastian, Giacomo Costalunga, Tim P Vogels, and
Daniela Vallentin. “Interplay between Syllable Duration and Pitch during Whistle
Matching in Wild Nightingales.” Current Biology. Elsevier, 2026. https://doi.org/10.1016/j.cub.2025.12.025.
ieee: J. S. Calderon Garcia, G. Costalunga, T. P. Vogels, and D. Vallentin, “Interplay
between syllable duration and pitch during whistle matching in wild nightingales,”
Current Biology, vol. 36, no. 3. Elsevier, p. 791–798.e6, 2026.
ista: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. 2026. Interplay
between syllable duration and pitch during whistle matching in wild nightingales.
Current Biology. 36(3), 791–798.e6.
mla: Calderon Garcia, Juan Sebastian, et al. “Interplay between Syllable Duration
and Pitch during Whistle Matching in Wild Nightingales.” Current Biology,
vol. 36, no. 3, Elsevier, 2026, p. 791–798.e6, doi:10.1016/j.cub.2025.12.025.
short: J.S. Calderon Garcia, G. Costalunga, T.P. Vogels, D. Vallentin, Current Biology
36 (2026) 791–798.e6.
das_tickbox: '1'
dataavailabilitystatement: "All data have been deposited at https://github.com/vallentinlab/NG-whistle-durations
and are publicly available as of the date of publication.\r\nAll original code has
been deposited at https://github.com/vallentinlab/NG-whistle-durations and is publicly
available as of the date of publication.\r\nAny additional information required
to reanalyze the data reported in this paper is available from the lead contact
upon request."
date_created: 2026-01-14T12:00:29Z
date_published: 2026-02-02T00:00:00Z
date_updated: 2026-07-27T10:48:35Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: GradSch
- _id: TiVo
doi: 10.1016/j.cub.2025.12.025
ec_funded: 1
external_id:
pmid:
- '41529680'
file:
- access_level: open_access
checksum: e17c3537193d5ab4886596d1a04f9b0e
content_type: application/pdf
creator: dernst
date_created: 2026-07-27T10:47:55Z
date_updated: 2026-07-27T10:47:55Z
file_id: '22416'
file_name: 2026_CurrentBiology_CalderonGarcia.pdf
file_size: 7120959
relation: main_file
success: 1
file_date_updated: 2026-07-27T10:47:55Z
has_accepted_license: '1'
intvolume: ' 36'
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 791-798.e6
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Interplay between syllable duration and pitch during whistle matching in wild
nightingales
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: 36
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19036'
abstract:
- lang: eng
text: Neuronal processing of external sensory input is shaped by internally generated
top–down information. In the neocortex, top–down projections primarily target
layer 1, which contains NDNF (neuron-derived neurotrophic factor)-expressing interneurons
and the dendrites of pyramidal cells. Here, we investigate the hypothesis that
NDNF interneurons shape cortical computations in an unconventional, layer-specific
way, by exerting presynaptic inhibition on synapses in layer 1 while leaving synapses
in deeper layers unaffected. We first confirm experimentally that in the auditory
cortex, synapses from somatostatin-expressing (SOM) onto NDNF neurons are indeed
modulated by ambient Gamma-aminobutyric acid (GABA). Shifting to a computational
model, we then show that this mechanism introduces a distinct mutual inhibition
motif between NDNF interneurons and the synaptic outputs of SOM interneurons.
This motif can control inhibition in a layer-specific way and introduces competition
between NDNF and SOM interneurons for dendritic inhibition onto pyramidal cells
on different timescales. NDNF interneurons can thereby control cortical information
flow by redistributing dendritic inhibition from fast to slow timescales and by
gating different sources of dendritic inhibition.
acknowledgement: "We thank all members of the Letzkus lab, the Sprekeler lab, and
the Vogels lab for discussions, U. Thirimanna for technical assistance, and K. Deisseroth
for generously sharing reagents. This work was supported by the German Research
Foundation (LE 3804/3-1, LE 3804/4-1, LE 3804/7-1, CRC-TRR 384/1 2024, - 514483642,
and 460088091) and the Wellcome Trust Senior Research Fellowship 214316/Z/18/Z.\r\nElectrophysiological
recordings, source code for simulations, and data analysis have been deposited in
GitHub (https://github.com/LNaumann/NDNF_control_inhibition_Naumann25) (62)."
article_number: e2408966122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Laura B
full_name: Naumann, Laura B
id: 81a3b706-8972-11ed-ae7b-8eff728700ca
last_name: Naumann
- first_name: Loreen
full_name: Hertäg, Loreen
last_name: Hertäg
- first_name: Jennifer
full_name: Müller, Jennifer
last_name: Müller
- first_name: Johannes J.
full_name: Letzkus, Johannes J.
last_name: Letzkus
- first_name: Henning
full_name: Sprekeler, Henning
last_name: Sprekeler
citation:
ama: Naumann LB, Hertäg L, Müller J, Letzkus JJ, Sprekeler H. Layer-specific control
of inhibition by NDNF interneurons. Proceedings of the National Academy of
Sciences. 2025;122(4). doi:10.1073/pnas.2408966122
apa: Naumann, L. B., Hertäg, L., Müller, J., Letzkus, J. J., & Sprekeler, H.
(2025). Layer-specific control of inhibition by NDNF interneurons. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2408966122
chicago: Naumann, Laura B, Loreen Hertäg, Jennifer Müller, Johannes J. Letzkus,
and Henning Sprekeler. “Layer-Specific Control of Inhibition by NDNF Interneurons.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2025. https://doi.org/10.1073/pnas.2408966122.
ieee: L. B. Naumann, L. Hertäg, J. Müller, J. J. Letzkus, and H. Sprekeler, “Layer-specific
control of inhibition by NDNF interneurons,” Proceedings of the National Academy
of Sciences, vol. 122, no. 4. National Academy of Sciences, 2025.
ista: Naumann LB, Hertäg L, Müller J, Letzkus JJ, Sprekeler H. 2025. Layer-specific
control of inhibition by NDNF interneurons. Proceedings of the National Academy
of Sciences. 122(4), e2408966122.
mla: Naumann, Laura B., et al. “Layer-Specific Control of Inhibition by NDNF Interneurons.”
Proceedings of the National Academy of Sciences, vol. 122, no. 4, e2408966122,
National Academy of Sciences, 2025, doi:10.1073/pnas.2408966122.
short: L.B. Naumann, L. Hertäg, J. Müller, J.J. Letzkus, H. Sprekeler, Proceedings
of the National Academy of Sciences 122 (2025).
date_created: 2025-02-17T09:20:19Z
date_published: 2025-01-22T00:00:00Z
date_updated: 2026-02-16T12:28:02Z
day: '22'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1073/pnas.2408966122
external_id:
isi:
- '001422380500004'
pmid:
- '39841147'
file:
- access_level: open_access
checksum: 636d5130724e3236ebf4fc658b3945fe
content_type: application/pdf
creator: dernst
date_created: 2025-02-17T14:46:18Z
date_updated: 2025-02-17T14:46:18Z
file_id: '19046'
file_name: 2025_PNAS_Naumann.pdf
file_size: 13726531
relation: main_file
success: 1
file_date_updated: 2025-02-17T14:46:18Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/LNaumann/NDNF_control_inhibition_Naumann25
scopus_import: '1'
status: public
title: Layer-specific control of inhibition by NDNF interneurons
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19068'
abstract:
- lang: eng
text: Whether or not the neuron emits a spike in response to stimulation by an excitatory
current pulse is determined by a strength-duration curve (SDC) for the pulse parameters.
The SDC is a dependence of the minimal pulse amplitude required to elicit the
spiking response on either the pulse duration or its decay time. Excitatory neurons
affect the others through pulses of excitatory postsynaptic current. A simple
yet plausible approximation for the time course of such a pulse is the alpha function,
with linear rise at the start and exponential decay at the end. However, an exact
analytical SDC for this case is hitherto not known, even for the leaky integrate-and-fire
(LIF) neuron, the simplest spiking neuron model used in practice. We have obtained
general SDC equations for the LIF neuron. Using the Lambert W function — a widely-implemented
special function, we have found the exact analytical SDC for the spiking response
of the LIF neuron stimulated by an excitatory current pulse in the form of the
alpha function. To compare results in a unified way, we have also derived the
analytical SDCs for (i) rectangular pulse, (ii) ascending ramp pulse, and (iii)
instantly rising and exponentially decaying pulse. In the limit of no leakage,
we show that the SDC is reduced to the classical hyperbola for all considered
cases.
acknowledgement: "The author thanks T.S. Zemskova and N.D. Efimova for verifying some
of the results. This work was supported by a European Research Council Consolidator
Grant (SYNAPSEEK, 819603, to Tim P. Vogels).\r\nThe Supplementary Material for this
article contains (i) the data for graphs in Figure 1 and (ii) ready-to-use MATLAB
codes for reproducing the data. It is available online at https://doi.org/10.6084/m9.figshare.24081849."
article_number: '100548'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alexander
full_name: Paraskevov, Alexander
id: d05e3c56-9262-11ed-9231-be692464e5ac
last_name: Paraskevov
citation:
ama: Paraskevov A. Analytical strength-duration curve for the spiking response of
the LIF neuron to an alpha-function-shaped excitatory current pulse. Results
in Applied Mathematics. 2025;25. doi:10.1016/j.rinam.2025.100548
apa: Paraskevov, A. (2025). Analytical strength-duration curve for the spiking response
of the LIF neuron to an alpha-function-shaped excitatory current pulse. Results
in Applied Mathematics. Elsevier. https://doi.org/10.1016/j.rinam.2025.100548
chicago: Paraskevov, Alexander. “Analytical Strength-Duration Curve for the Spiking
Response of the LIF Neuron to an Alpha-Function-Shaped Excitatory Current Pulse.”
Results in Applied Mathematics. Elsevier, 2025. https://doi.org/10.1016/j.rinam.2025.100548.
ieee: A. Paraskevov, “Analytical strength-duration curve for the spiking response
of the LIF neuron to an alpha-function-shaped excitatory current pulse,” Results
in Applied Mathematics, vol. 25. Elsevier, 2025.
ista: Paraskevov A. 2025. Analytical strength-duration curve for the spiking response
of the LIF neuron to an alpha-function-shaped excitatory current pulse. Results
in Applied Mathematics. 25, 100548.
mla: Paraskevov, Alexander. “Analytical Strength-Duration Curve for the Spiking
Response of the LIF Neuron to an Alpha-Function-Shaped Excitatory Current Pulse.”
Results in Applied Mathematics, vol. 25, 100548, Elsevier, 2025, doi:10.1016/j.rinam.2025.100548.
short: A. Paraskevov, Results in Applied Mathematics 25 (2025).
corr_author: '1'
das_tickbox: '1'
date_created: 2025-02-23T23:01:55Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2026-06-22T08:29:37Z
day: '01'
ddc:
- '570'
- '510'
department:
- _id: TiVo
doi: 10.1016/j.rinam.2025.100548
ec_funded: 1
file:
- access_level: open_access
checksum: 58fd02e951857859f39d06661a27bcc9
content_type: application/pdf
creator: dernst
date_created: 2025-02-24T13:18:47Z
date_updated: 2025-02-24T13:18:47Z
file_id: '19083'
file_name: 2025_ResultsApplMath_Paraskevov.pdf
file_size: 853322
relation: main_file
success: 1
file_date_updated: 2025-02-24T13:18:47Z
has_accepted_license: '1'
intvolume: ' 25'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Results in Applied Mathematics
publication_identifier:
eissn:
- 2590-0374
publication_status: published
publisher: Elsevier
related_material:
link:
- relation: software
url: https://doi.org/10.6084/m9.figshare.24081849
- relation: erratum
url: https://doi.org/10.1016/j.rinam.2026.100713
scopus_import: '1'
status: public
title: Analytical strength-duration curve for the spiking response of the LIF neuron
to an alpha-function-shaped excitatory current pulse
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: 25
year: '2025'
...
---
APC_amount: 3237,62 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '19640'
abstract:
- lang: eng
text: Synaptic plasticity is a key player in the brain’s life-long learning abilities.
However, due to experimental limitations, the mechanistic link between synaptic
plasticity rules and the network-level computations they enable remain opaque.
Here we use evolutionary strategies (ES) to meta learn local co-active plasticity
rules in large recurrent spiking networks with excitatory (E) and inhibitory (I)
neurons, using parameterizations of increasing complexity. We discover rules that
robustly stabilize network dynamics for all four synapse types acting in isolation
(E-to-E, E-to-I, I-to-E and I-to-I). More complex functions such as familiarity
detection can also be included in the search constraints. However, our meta learning
strategy begins to fail for co-active rules of increasing complexity, as it is
challenging to devise loss functions that effectively constrain network dynamics
to plausible solutions a priori. Moreover, in line with previous work, we can
find multiple degenerate solutions with identical network behaviour. As a local
optimization strategy, ES provides one solution at a time and makes exploration
of this degeneracy cumbersome. Regardless, we can glean the interdependecies of
various plasticity parameters by considering the covariance matrix learned alongside
the optimal rule with ES. Our work provides a proof of principle for the success
of machine-learning-guided discovery of plasticity rules in large spiking networks,
and points at the necessity of more elaborate search strategies going forward.
acknowledgement: "We would like to thank Chaitanya Chintaluri, Nicoleta Condruz and
Douglas Feitosa Tomé for insightful discussions. This project has received funding
from the HORIZON EUROPE European Research Council (ERC) consolidator grant\r\n(SYNAPSEEK,
awarded to TV), a Wellcome Trust Sir Henry Dale Research Fellowship (WT100000, awarded
to TV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z, awarded to TV),
and a Sir Henry Wellcome\r\nFellowship (110124/Z/15/Z, awarded to FZ). The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript."
article_number: e1012910
article_processing_charge: Yes
article_type: original
author:
- first_name: Basile J
full_name: Confavreux, Basile J
id: C7610134-B532-11EA-BD9F-F5753DDC885E
last_name: Confavreux
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Friedemann
full_name: Zenke, Friedemann
last_name: Zenke
- first_name: Henning
full_name: Sprekeler, Henning
last_name: Sprekeler
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Confavreux BJ, Agnes EJ, Zenke F, Sprekeler H, Vogels TP. Balancing complexity,
performance and plausibility to meta learn plasticity rules in recurrent spiking
networks. PLoS Computational Biology. 2025;21(4). doi:10.1371/journal.pcbi.1012910
apa: Confavreux, B. J., Agnes, E. J., Zenke, F., Sprekeler, H., & Vogels, T.
P. (2025). Balancing complexity, performance and plausibility to meta learn plasticity
rules in recurrent spiking networks. PLoS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1012910
chicago: Confavreux, Basile J, Everton J. Agnes, Friedemann Zenke, Henning Sprekeler,
and Tim P Vogels. “Balancing Complexity, Performance and Plausibility to Meta
Learn Plasticity Rules in Recurrent Spiking Networks.” PLoS Computational Biology.
Public Library of Science, 2025. https://doi.org/10.1371/journal.pcbi.1012910.
ieee: B. J. Confavreux, E. J. Agnes, F. Zenke, H. Sprekeler, and T. P. Vogels, “Balancing
complexity, performance and plausibility to meta learn plasticity rules in recurrent
spiking networks,” PLoS Computational Biology, vol. 21, no. 4. Public Library
of Science, 2025.
ista: Confavreux BJ, Agnes EJ, Zenke F, Sprekeler H, Vogels TP. 2025. Balancing
complexity, performance and plausibility to meta learn plasticity rules in recurrent
spiking networks. PLoS Computational Biology. 21(4), e1012910.
mla: Confavreux, Basile J., et al. “Balancing Complexity, Performance and Plausibility
to Meta Learn Plasticity Rules in Recurrent Spiking Networks.” PLoS Computational
Biology, vol. 21, no. 4, e1012910, Public Library of Science, 2025, doi:10.1371/journal.pcbi.1012910.
short: B.J. Confavreux, E.J. Agnes, F. Zenke, H. Sprekeler, T.P. Vogels, PLoS Computational
Biology 21 (2025).
corr_author: '1'
date_created: 2025-05-04T22:02:31Z
date_published: 2025-04-24T00:00:00Z
date_updated: 2026-05-06T13:17:52Z
day: '24'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1012910
ec_funded: 1
external_id:
isi:
- '001474257000002'
pmid:
- '40273284 '
file:
- access_level: open_access
checksum: 6437a1aab52813ab7e310e3b4fb36e3b
content_type: application/pdf
creator: dernst
date_created: 2025-05-05T11:17:49Z
date_updated: 2025-05-05T11:17:49Z
file_id: '19654'
file_name: 2025_PLoSCompBio_Confavreux.pdf
file_size: 9771636
relation: main_file
success: 1
file_date_updated: 2025-05-05T11:17:49Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/VogelsLab/SpikES
scopus_import: '1'
status: public
title: Balancing complexity, performance and plausibility to meta learn plasticity
rules in recurrent spiking networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19794'
abstract:
- lang: eng
text: Status epilepticus (SE), seizures lasting beyond five minutes, is a medical
emergency commonly treated with benzodiazepines which enhance GABAA receptor (GABAAR)
conductance. Despite widespread use, benzodiazepines fail in over one-third of
patients, potentially due to seizure-induced disruption of neuronal chloride (Cl−)
homeostasis. Understanding these changes at a network level is crucial for improving
clinical translation. Here, we address this using a large-scale spiking neural
network model incorporating Cl− dynamics, informed by clinical EEG and experimental
slice recordings. Our simulations confirm that the GABAAR reversal potential (EGABA)
dictates the pro- or anti-seizure effect of GABAAR conductance modulation, with
high EGABA rendering benzodiazepines ineffective or excitatory. We show SE-like
activity and EGABA depend non-linearly on Cl− extrusion efficacy and GABAAR conductance.
Critically, cell-type specific manipulations reveal that pyramidal cell, not interneuron,
Cl− extrusion predominantly determines the severity of SE activity and the response
to simulated benzodiazepines. Leveraging these mechanistic insights, we develop
a predictive framework mapping network states to Cl− extrusion capacity and GABAergic
load, yielding a proposed decision-making strategy to guide therapeutic interventions
based on initial treatment response. This work identifies pyramidal cell Cl− handling
as a key therapeutic target and demonstrates the utility of biophysically detailed
network models for optimising SE treatment protocols.
acknowledgement: 'The research leading to these results has received support from
the National Research Foundation of South Africa, the Deutscher Akademischer Austauschdienst,
NOMIS Foundation, NVIDIA Academic Program, the University of Cape Town, the Anna
Mueller Grocholski Foundation, the Swiss National Science Foundation (SNSF: 208184),
the Gabriel Foundation, a Wellcome Trust Seed Award (214042/Z/18/Z), the South African
Medical Research Council and the FLAIR Fellowship Programme (FLR\R1\190829): a partnership
between the African Academy of Sciences and the Royal Society funded by the UK Government''s
Global Challenges Research Fund and a Wellcome Trust International Intermediate
Fellowship (222968/Z/21/Z).'
article_number: '106966'
article_processing_charge: Yes
article_type: original
author:
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Richard J.
full_name: Burman, Richard J.
last_name: Burman
- first_name: Tommaso
full_name: Fedele, Tommaso
last_name: Fedele
- first_name: Georgia
full_name: Ramantani, Georgia
last_name: Ramantani
- first_name: Richard E.
full_name: Rosch, Richard E.
last_name: Rosch
- first_name: Henning
full_name: Sprekeler, Henning
last_name: Sprekeler
- first_name: Joseph V.
full_name: Raimondo, Joseph V.
last_name: Raimondo
citation:
ama: Currin C, Burman RJ, Fedele T, et al. Network models incorporating chloride
dynamics predict optimal strategies for terminating status epilepticus. Neurobiology
of Disease. 2025;212. doi:10.1016/j.nbd.2025.106966
apa: Currin, C., Burman, R. J., Fedele, T., Ramantani, G., Rosch, R. E., Sprekeler,
H., & Raimondo, J. V. (2025). Network models incorporating chloride dynamics
predict optimal strategies for terminating status epilepticus. Neurobiology
of Disease. Elsevier. https://doi.org/10.1016/j.nbd.2025.106966
chicago: Currin, Christopher, Richard J. Burman, Tommaso Fedele, Georgia Ramantani,
Richard E. Rosch, Henning Sprekeler, and Joseph V. Raimondo. “Network Models Incorporating
Chloride Dynamics Predict Optimal Strategies for Terminating Status Epilepticus.”
Neurobiology of Disease. Elsevier, 2025. https://doi.org/10.1016/j.nbd.2025.106966.
ieee: C. Currin et al., “Network models incorporating chloride dynamics predict
optimal strategies for terminating status epilepticus,” Neurobiology of Disease,
vol. 212. Elsevier, 2025.
ista: Currin C, Burman RJ, Fedele T, Ramantani G, Rosch RE, Sprekeler H, Raimondo
JV. 2025. Network models incorporating chloride dynamics predict optimal strategies
for terminating status epilepticus. Neurobiology of Disease. 212, 106966.
mla: Currin, Christopher, et al. “Network Models Incorporating Chloride Dynamics
Predict Optimal Strategies for Terminating Status Epilepticus.” Neurobiology
of Disease, vol. 212, 106966, Elsevier, 2025, doi:10.1016/j.nbd.2025.106966.
short: C. Currin, R.J. Burman, T. Fedele, G. Ramantani, R.E. Rosch, H. Sprekeler,
J.V. Raimondo, Neurobiology of Disease 212 (2025).
corr_author: '1'
date_created: 2025-06-08T22:01:22Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-12-30T08:36:36Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.nbd.2025.106966
external_id:
isi:
- '001501576500001'
file:
- access_level: open_access
checksum: abe215be676ed14e9a37fb78b6a5a610
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T08:35:41Z
date_updated: 2025-12-30T08:35:41Z
file_id: '20896'
file_name: 2025_NeurobioDisease_Currin.pdf
file_size: 7063352
relation: main_file
success: 1
file_date_updated: 2025-12-30T08:35:41Z
has_accepted_license: '1'
intvolume: ' 212'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Neurobiology of Disease
publication_identifier:
eissn:
- 1095-953X
issn:
- 0969-9961
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Network models incorporating chloride dynamics predict optimal strategies for
terminating status epilepticus
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2025'
...
---
APC_amount: 4910,08 EUR
OA_place: publisher
OA_type: gold
_id: '8125'
abstract:
- lang: eng
text: "Biological memory is known to be flexible—memory formation and recall depend
on factors such as the behavioral context of the organism. However, this property
is often ignored in associative memory models, leaving it unclear how memories
can be organized and recalled when subject to contextual control. Because of the
lack of a rigorous analytical framework, it is also unknown how contextual control
affects memory stability, storage capacity, and information content. Here, we
bring the dynamic nature of memory to the fore by introducing a novel model of
associative memory, which we refer to as the context-modular memory network. In
our model, stored memory patterns are associated to one of several background
network states, or contexts. Memories are accessible when their corresponding
context is active, and are otherwise inaccessible. Context modulates the effective
network connectivity by imposing a specific\r\nconfiguration of neuronal and synaptic
gating—gated neurons (synapses) have their activity (weights) momentarily silenced,
thereby reducing interference from memories belonging to other contexts. Memory
patterns are randomly and independently chosen, while neuronal and synaptic gates
may be selected randomly or optimized through a process of contextual synaptic
refinement. Through analytic and numerical results, we show that context-modular
memory networks can exhibit both improved memory capacity and differential control
of memory stability with random gating (especially for neuronal gating). For contextual
synaptic refinement, we devise a method in which synapses are gated off for a
given context if they destabilize the memory patterns in that context, drastically
improving memory capacity and enabling even more precise control over memory stability.
Notably, synaptic refinement allows for patterns to be\r\naccessible in multiple
contexts, stabilizing memory patterns even for weight matrices that alone do not
contain any information about the memory patterns, such as Gaussian random matrices.
Overall, our model integrates recent ideas about context-dependent memory organization
with classic associative memory models and proposes a rigorous theory which can
act as a framework for future work. Furthermore, our work carries important implications
for the understanding of biological memory storage and recall in the brain, such
as highlighting an intriguing trade-off between memory capacity and accessibility."
acknowledgement: "We thank Helen Barron, Vezha Boboeva, Adam Packer, João Sacramento,
Andrew Saxe, Misha Tsodyks, and Friedemann Zenke for helpful comments at various
stages of this work, and Rubem Erichsen, Jr. for carefully reading the manuscript
and valuable comments. This work was\r\nsupported by a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society [No. WT100000 (W. F. P., E. J. A., and
T. P. V.)], a Wellcome Trust Senior Research Fellowship [No. 214316/Z/18/Z (E. J.
A. and T. P. V.)], and a Research Project Grant by the Leverhulme Trust\r\n[No.
RPG-2016-446 (E. J. A.)]. "
article_number: '011057'
article_processing_charge: Yes
article_type: original
author:
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in
associative memory networks with context-dependent neuronal and synaptic gating.
Physical Review X. 2025;15. doi:10.1103/PhysRevX.15.011057
apa: Podlaski, W. F., Agnes, E. J., & Vogels, T. P. (2025). High capacity and
dynamic accessibility in associative memory networks with context-dependent neuronal
and synaptic gating. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.15.011057
chicago: Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity
and Dynamic Accessibility in Associative Memory Networks with Context-Dependent
Neuronal and Synaptic Gating.” Physical Review X. American Physical Society,
2025. https://doi.org/10.1103/PhysRevX.15.011057.
ieee: W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic
accessibility in associative memory networks with context-dependent neuronal and
synaptic gating,” Physical Review X, vol. 15. American Physical Society,
2025.
ista: Podlaski WF, Agnes EJ, Vogels TP. 2025. High capacity and dynamic accessibility
in associative memory networks with context-dependent neuronal and synaptic gating.
Physical Review X. 15, 011057.
mla: Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative
Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” Physical
Review X, vol. 15, 011057, American Physical Society, 2025, doi:10.1103/PhysRevX.15.011057.
short: W.F. Podlaski, E.J. Agnes, T.P. Vogels, Physical Review X 15 (2025).
corr_author: '1'
date_created: 2020-07-16T12:24:28Z
date_published: 2025-03-13T00:00:00Z
date_updated: 2026-05-06T12:44:27Z
day: '13'
ddc:
- '530'
department:
- _id: TiVo
doi: 10.1103/PhysRevX.15.011057
external_id:
isi:
- '001451378900002'
file:
- access_level: open_access
checksum: 1f27ee469ab51a3e1ce1e2df0022e81d
content_type: application/pdf
creator: dernst
date_created: 2025-03-20T12:47:17Z
date_updated: 2025-03-20T12:47:17Z
file_id: '19432'
file_name: 2025_PhysReviewX_Podlaski.pdf
file_size: 1373704
relation: main_file
success: 1
file_date_updated: 2025-03-20T12:47:17Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
locked: '1'
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/wpodlaski/contextual-memory-nets
scopus_import: '1'
status: public
title: High capacity and dynamic accessibility in associative memory networks with
context-dependent neuronal and synaptic gating
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: 15
year: '2025'
...
---
OA_place: publisher
_id: '20735'
abstract:
- lang: eng
text: "Left–right alternation is a defining feature of spinal locomotor circuits,
yet the level of neuronal\r\ndetail required to generate and maintain this pattern
remains unclear. This thesis investigates how\r\nmodels spanning multiple levels
of abstraction—from biophysically detailed Hodgkin–Huxley (HH)\r\nneurons to adaptive
integrate–and–fire (I&F) formulations and synfire-chain modules—can account\r\nfor
the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole.
The guiding\r\nhypothesis is that a small set of neuronal mechanisms is sufficient
to reproduce the essential features\r\nof rhythmic alternation, and that moving
between modeling scales helps distinguish core principles\r\nfrom biological detail.\r\nA
minimal bilateral HH network comprising only four canonical neuron classes—excitatory\r\ndescending
interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory\r\ninterneurons
(aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce\r\nexperimentally
observed firing modes, the model demonstrated that rebound-prone dIN excitability,\r\ncontralateral
inhibition and modest electrical coupling are sufficient to generate stable alternating\r\nactivity,
even in very small networks. These results motivated the transition to simpler
models\r\ncapable of efficient analysis and scaling.\r\nAdaptive exponential I&F
(AdEx) neurons were calibrated to physiological recordings using\r\nsimulation-based
inference, yielding tonic and phasic/rebound templates that preserved the key\r\ndynamical
signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying\r\nsingle-spike
responses and rebound firing in dINs. At network level, the I&F models robustly\r\nreproduced
left–right alternation, while highlighting constraints on synaptic kinetics and
adaptation\r\nneeded to avoid multi-spike responses.\r\nFinally, a synfire-chain
framework provided a complementary, timing-centric perspective, demonstrating
how precise spike synchrony, synaptic delays and minimal inhibitory coupling can
generate\r\nalternating left–right sequences in a feedforward setting. Together,
these approaches converge on a\r\ncommon conclusion: rebound-prone ipsilateral
excitation combined with precisely timed contralateral inhibition constitutes
a sufficient substrate for alternating spinal rhythms.\r\nBy integrating bottom-up
and top-down modeling strategies, this thesis provides a unified, extensible framework
for studying spinal pattern generation. The results show that essential locomotor\r\ndynamics
can be captured across multiple abstraction levels, offering both mechanistic
insight and\r\npractical tools for future data-driven investigations of spinal
circuit development, robustness and\r\nmodulation."
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Alexia C
full_name: Wilson, Alexia C
id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d
last_name: Wilson
orcid: 0000-0001-6191-1367
citation:
ama: 'Wilson AC. Modelling the spinal cord of a tadpole: Exploring different ways
to model the spinal cord in the Xenopus frog. 2025. doi:10.15479/AT-ISTA-20735'
apa: 'Wilson, A. C. (2025). Modelling the spinal cord of a tadpole: Exploring
different ways to model the spinal cord in the Xenopus frog. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20735'
chicago: 'Wilson, Alexia C. “Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog.” Institute of Science and Technology
Austria, 2025. https://doi.org/10.15479/AT-ISTA-20735.'
ieee: 'A. C. Wilson, “Modelling the spinal cord of a tadpole: Exploring different
ways to model the spinal cord in the Xenopus frog,” Institute of Science and Technology
Austria, 2025.'
ista: 'Wilson AC. 2025. Modelling the spinal cord of a tadpole: Exploring different
ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology
Austria.'
mla: 'Wilson, Alexia C. Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog. Institute of Science and
Technology Austria, 2025, doi:10.15479/AT-ISTA-20735.'
short: 'A.C. Wilson, Modelling the Spinal Cord of a Tadpole: Exploring Different
Ways to Model the Spinal Cord in the Xenopus Frog, Institute of Science and Technology
Austria, 2025.'
corr_author: '1'
date_created: 2025-12-08T09:49:41Z
date_published: 2025-12-09T00:00:00Z
date_updated: 2026-07-29T12:55:12Z
day: '09'
ddc:
- '570'
- '596'
- '005'
degree_awarded: MS
department:
- _id: GradSch
- _id: TiVo
- _id: LoSw
doi: 10.15479/AT-ISTA-20735
doi_confirm: '1'
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language:
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month: '12'
oa: 1
oa_version: Published Version
page: '110'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13097'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
title: 'Modelling the spinal cord of a tadpole: Exploring different ways to model
the spinal cord in the Xenopus frog'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '14841'
abstract:
- lang: eng
text: De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium
(K+) channel subunit Kv3.2 are a recently described cause of developmental and
epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr)
was identified via exome sequencing in a patient with DEE. Relative to wild-type
Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing
shift in the voltage dependence of activation, accelerated activation, and delayed
deactivation consistent with a relative stabilization of the open conformation,
along with increased current density. Leveraging the cryogenic electron microscopy
(cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong
π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix
of the T1 domain promotes a relative stabilization of the open conformation of
the channel, which underlies the observed gain of function. A multicompartment
computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking
γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the
Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition
in cerebral cortex circuits to explain the resulting epilepsy.
acknowledgement: This work was supported by an ERC Consolidator Grant (SYNAPSEEK)
to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria
to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH
NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G.
The computations were enabled by resources provided by the Swedish National Infrastructure
for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal
Institute of Technology, partially funded by the Swedish Research Council through
grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion
of the project.
article_number: e2307776121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jerome
full_name: Clatot, Jerome
last_name: Clatot
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Qiansheng
full_name: Liang, Qiansheng
last_name: Liang
- first_name: Tanadet
full_name: Pipatpolkai, Tanadet
last_name: Pipatpolkai
- first_name: Shavonne L.
full_name: Massey, Shavonne L.
last_name: Massey
- first_name: Ingo
full_name: Helbig, Ingo
last_name: Helbig
- first_name: Lucie
full_name: Delemotte, Lucie
last_name: Delemotte
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Manuel
full_name: Covarrubias, Manuel
last_name: Covarrubias
- first_name: Ethan M.
full_name: Goldberg, Ethan M.
last_name: Goldberg
citation:
ama: Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links
an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(3). doi:10.1073/pnas.2307776121
apa: Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig,
I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated
KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2307776121
chicago: Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai,
Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias,
and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated
KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2307776121.
ieee: J. Clatot et al., “A structurally precise mechanism links an epilepsy-associated
KCNC2 potassium channel mutation to interneuron dysfunction,” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 3. National Academy of Sciences, 2024.
ista: Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte
L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism
links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction.
Proceedings of the National Academy of Sciences of the United States of America.
121(3), e2307776121.
mla: Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated
KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 3, e2307776121, National Academy of Sciences, 2024, doi:10.1073/pnas.2307776121.
short: J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L.
Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National
Academy of Sciences of the United States of America 121 (2024).
date_created: 2024-01-21T23:00:56Z
date_published: 2024-01-16T00:00:00Z
date_updated: 2025-09-04T11:47:47Z
day: '16'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1073/pnas.2307776121
ec_funded: 1
external_id:
isi:
- '001167401000001'
pmid:
- '38194456'
file:
- access_level: open_access
checksum: f498c643be81895dd3a69ee90115a782
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T13:51:16Z
date_updated: 2025-04-23T13:51:16Z
file_id: '19613'
file_name: 2024_PNAS_Clatot.pdf
file_size: 3060109
relation: main_file
success: 1
file_date_updated: 2025-04-23T13:51:16Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '3'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: 'https://github.com/ChrisCurrin/pv-kcnc2 '
scopus_import: '1'
status: public
title: A structurally precise mechanism links an epilepsy-associated KCNC2 potassium
channel mutation to interneuron dysfunction
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
_id: '14887'
abstract:
- lang: eng
text: 'Episodic memories are encoded by experience-activated neuronal ensembles
that remain necessary and sufficient for recall. However, the temporal evolution
of memory engrams after initial encoding is unclear. In this study, we employed
computational and experimental approaches to examine how the neural composition
and selectivity of engrams change with memory consolidation. Our spiking neural
network model yielded testable predictions: memories transition from unselective
to selective as neurons drop out of and drop into engrams; inhibitory activity
during recall is essential for memory selectivity; and inhibitory synaptic plasticity
during memory consolidation is critical for engrams to become selective. Using
activity-dependent labeling, longitudinal calcium imaging and a combination of
optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted
contextual fear conditioning experiments that supported our model’s predictions.
Our results reveal that memory engrams are dynamic and that changes in engram
composition mediated by inhibitory plasticity are crucial for the emergence of
memory selectivity.'
acknowledgement: We thank S. Erisken from Inscopix for helping us establish in vivo
one-photon calcium imaging for this work. We thank K. Su at Tsinghua University
for assistance with this work. This work was funded by the President’s PhD Scholarship
from Imperial College London (D.F.T.), the Wellcome Trust (225412/Z/22/Z) (S.S.),
the Biotechnology and Biological Sciences Research Council (BB/N013956/1 and BB/N019008/1)
(C.C.), the Wellcome Trust (200790/Z/16/Z) (C.C.), the Simons Foundation (564408)
(C.C.) and the Engineering and Physical Sciences Research Council (EP/R035806/1)
(CC). The School of Life Sciences and the IDG/McGovern Institute for Brain Research
supported Y.Z. The Warren Alpert Distinguished Scholar Award and National Institutes
of Health 1K99NS125131-01 supported D.S.R.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Douglas
full_name: Feitosa Tomé, Douglas
id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2
last_name: Feitosa Tomé
- first_name: Ying
full_name: Zhang, Ying
last_name: Zhang
- first_name: Tomomi
full_name: Aida, Tomomi
last_name: Aida
- first_name: Olivia
full_name: Mosto, Olivia
last_name: Mosto
- first_name: Yifeng
full_name: Lu, Yifeng
last_name: Lu
- first_name: Mandy
full_name: Chen, Mandy
last_name: Chen
- first_name: Sadra
full_name: Sadeh, Sadra
last_name: Sadeh
- first_name: Dheeraj S.
full_name: Roy, Dheeraj S.
last_name: Roy
- first_name: Claudia
full_name: Clopath, Claudia
last_name: Clopath
citation:
ama: Feitosa Tomé D, Zhang Y, Aida T, et al. Dynamic and selective engrams emerge
with memory consolidation. Nature Neuroscience. 2024;27:561-572. doi:10.1038/s41593-023-01551-w
apa: Feitosa Tomé, D., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., … Clopath,
C. (2024). Dynamic and selective engrams emerge with memory consolidation. Nature
Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01551-w
chicago: Feitosa Tomé, Douglas, Ying Zhang, Tomomi Aida, Olivia Mosto, Yifeng Lu,
Mandy Chen, Sadra Sadeh, Dheeraj S. Roy, and Claudia Clopath. “Dynamic and Selective
Engrams Emerge with Memory Consolidation.” Nature Neuroscience. Springer
Nature, 2024. https://doi.org/10.1038/s41593-023-01551-w.
ieee: D. Feitosa Tomé et al., “Dynamic and selective engrams emerge with
memory consolidation,” Nature Neuroscience, vol. 27. Springer Nature, pp.
561–572, 2024.
ista: Feitosa Tomé D, Zhang Y, Aida T, Mosto O, Lu Y, Chen M, Sadeh S, Roy DS, Clopath
C. 2024. Dynamic and selective engrams emerge with memory consolidation. Nature
Neuroscience. 27, 561–572.
mla: Feitosa Tomé, Douglas, et al. “Dynamic and Selective Engrams Emerge with Memory
Consolidation.” Nature Neuroscience, vol. 27, Springer Nature, 2024, pp.
561–72, doi:10.1038/s41593-023-01551-w.
short: D. Feitosa Tomé, Y. Zhang, T. Aida, O. Mosto, Y. Lu, M. Chen, S. Sadeh, D.S.
Roy, C. Clopath, Nature Neuroscience 27 (2024) 561–572.
corr_author: '1'
date_created: 2024-01-28T23:01:43Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-04-23T07:40:21Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1038/s41593-023-01551-w
external_id:
isi:
- '001145442300001'
pmid:
- '38243089'
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checksum: c509fcad757e4c1c153e857e55c20083
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creator: dernst
date_created: 2024-07-16T12:15:19Z
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month: '03'
oa: 1
oa_version: Published Version
page: 561-572
pmid: 1
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
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publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: Dynamic and selective engrams emerge with memory consolidation
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: 27
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15171'
abstract:
- lang: eng
text: The brain’s functionality is developed and maintained through synaptic plasticity.
As synapses undergo plasticity, they also affect each other. The nature of such
‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses
must be monitored simultaneously. To help understand the experimentally observed
phenomena, we introduce a framework that formalizes synaptic co-dependency between
different connection types. The resulting model explains how inhibition can gate
excitatory plasticity while neighboring excitatory–excitatory interactions determine
the strength of long-term potentiation. Furthermore, we show how the interplay
between excitatory and inhibitory synapses can account for the quick rise and
long-term stability of a variety of synaptic weight profiles, such as orientation
tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks,
co-dependent plasticity produces rich and stable motor cortex-like dynamics with
high input sensitivity. Our results suggest an essential role for the neighborly
synaptic interaction during learning, connecting micro-level physiology with network-wide
phenomena.
acknowledgement: We thank C. Currin, B. Podlaski and the members of the Vogels group
for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project
Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship
from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust
Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council
Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access,
the authors have applied a CC BY public copyright license to any author accepted
manuscript version arising from this submission. Open access funding provided by
University of Basel.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts
for quick, stable and long-lasting memories in biological networks. Nature
Neuroscience. 2024;27:964-974. doi:10.1038/s41593-024-01597-4
apa: Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory
plasticity accounts for quick, stable and long-lasting memories in biological
networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4
chicago: Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory
Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological
Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.
ieee: E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity
accounts for quick, stable and long-lasting memories in biological networks,”
Nature Neuroscience, vol. 27. Springer Nature, pp. 964–974, 2024.
ista: Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity
accounts for quick, stable and long-lasting memories in biological networks. Nature
Neuroscience. 27, 964–974.
mla: Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory
Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological
Networks.” Nature Neuroscience, vol. 27, Springer Nature, 2024, pp. 964–74,
doi:10.1038/s41593-024-01597-4.
short: E.J. Agnes, T.P. Vogels, Nature Neuroscience 27 (2024) 964–974.
date_created: 2024-03-24T23:01:00Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-04T13:06:06Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1038/s41593-024-01597-4
ec_funded: 1
external_id:
isi:
- '001190081400001'
pmid:
- '38509348 '
file:
- access_level: open_access
checksum: dfca68a24749575b912b3a78a7de4516
content_type: application/pdf
creator: dernst
date_created: 2025-06-25T08:45:32Z
date_updated: 2025-06-25T08:45:32Z
file_id: '19902'
file_name: 2025_NatureNeuroscience_Agnes.pdf
file_size: 10508018
relation: main_file
success: 1
file_date_updated: 2025-06-25T08:45:32Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 964-974
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Nature Neuroscience
publication_identifier:
eissn:
- 1546-1726
issn:
- 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Co-dependent excitatory and inhibitory plasticity accounts for quick, stable
and long-lasting memories in biological networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 27
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15258'
abstract:
- lang: eng
text: Inclusion at academic events is facing increased scrutiny as the communities
these events serve raise their expectations for who can practically attend. Active
efforts in recent years to bring more diversity to academic events have brought
progress and created momentum. However, we must reflect on these efforts and determine
which underrepresented groups are being disadvantaged. Inclusion at academic events
is important to ensure diversity of discourse and opinion, to help build networks,
and to avoid academic siloing. All of these contribute to the development of a
robust and resilient academic field. We have developed these Ten Simple Rules
both to amplify the voices that have been speaking out and to celebrate the progress
of many Equity, Diversity, and Inclusivity practices that continue to drive the
organisation of academic events. The Rules aim to raise awareness as well as provide
actionable suggestions and tools to support these initiatives further. This aims
to support academic organisations such as the Deep Learning Indaba, Neuromatch
Academy, the IBRO-Simons Computational Neuroscience Imbizo, Biodiversity Information
Standards (TDWG), Arabs in Neuroscience, FAIRPoints, and OLS (formerly Open Life
Science). This article is a call to action for organisers to reevaluate the impact
and reach of their inclusive practices.
acknowledgement: "We would like to recognise the feedback and ideas shared with us
by all attendees during the\r\nfocus groups that contributed to the development
of this paper. Acknowledgements are given\r\nto Elisee Jafsia, Umar Farouk Ahmad,
Zohra Slim, Mizanur Rahman, Rev. Katie Tupling,\r\nChristopher Emmanuel, Abdalrhman
Mostafa, Pradeep Eranti, Toby Hodges, Avishkar\r\nBhoopchand, and Carolyn Dickson.
We would like to thank our community members and\r\nacknowledge their bravery for
sharing their stories that shaped the narrative of these Ten Simple\r\nRules. The
stories shared with us formed the case studies, and while they are anonymous\r\nfor
privacy and protection reasons, it is these stories that were on our mind during
the entire\r\nprocess and kept us going. We acknowledge the efforts of the organisers
that contribute to the\r\nhighly successful events that are the inspiration for
the ideas presented here: the Deep\r\nLearning Indaba, Neuromatch Academy, the IBRO
Simons Computational Neuroscience\r\nImbizo, and OLS. OLS also supported this project
through their mentorship programme,\r\nOpen Seeds."
article_number: e1011797
article_processing_charge: Yes
article_type: original
author:
- first_name: Siobhan Mackenzie
full_name: Hall, Siobhan Mackenzie
last_name: Hall
- first_name: Daniel
full_name: Kochin, Daniel
last_name: Kochin
- first_name: Carmel
full_name: Carne, Carmel
last_name: Carne
- first_name: Patricia
full_name: Herterich, Patricia
last_name: Herterich
- first_name: Kristen Lenay
full_name: Lewers, Kristen Lenay
last_name: Lewers
- first_name: Mohamed
full_name: Abdelhack, Mohamed
last_name: Abdelhack
- first_name: Arun
full_name: Ramasubramanian, Arun
last_name: Ramasubramanian
- first_name: Juno Felecia
full_name: Michael Alphonse, Juno Felecia
last_name: Michael Alphonse
- first_name: Visotheary
full_name: Ung, Visotheary
last_name: Ung
- first_name: Sara
full_name: El-Gebali, Sara
last_name: El-Gebali
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Esther
full_name: Plomp, Esther
last_name: Plomp
- first_name: Rachel
full_name: Thompson, Rachel
last_name: Thompson
- first_name: Malvika
full_name: Sharan, Malvika
last_name: Sharan
citation:
ama: Hall SM, Kochin D, Carne C, et al. Ten simple rules for pushing boundaries
of inclusion at academic events. PLOS Computational Biology. 2024;20(3).
doi:10.1371/journal.pcbi.1011797
apa: Hall, S. M., Kochin, D., Carne, C., Herterich, P., Lewers, K. L., Abdelhack,
M., … Sharan, M. (2024). Ten simple rules for pushing boundaries of inclusion
at academic events. PLOS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1011797
chicago: Hall, Siobhan Mackenzie, Daniel Kochin, Carmel Carne, Patricia Herterich,
Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, et al. “Ten Simple
Rules for Pushing Boundaries of Inclusion at Academic Events.” PLOS Computational
Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011797.
ieee: S. M. Hall et al., “Ten simple rules for pushing boundaries of inclusion
at academic events,” PLOS Computational Biology, vol. 20, no. 3. Public
Library of Science, 2024.
ista: Hall SM, Kochin D, Carne C, Herterich P, Lewers KL, Abdelhack M, Ramasubramanian
A, Michael Alphonse JF, Ung V, El-Gebali S, Currin C, Plomp E, Thompson R, Sharan
M. 2024. Ten simple rules for pushing boundaries of inclusion at academic events.
PLOS Computational Biology. 20(3), e1011797.
mla: Hall, Siobhan Mackenzie, et al. “Ten Simple Rules for Pushing Boundaries of
Inclusion at Academic Events.” PLOS Computational Biology, vol. 20, no.
3, e1011797, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011797.
short: S.M. Hall, D. Kochin, C. Carne, P. Herterich, K.L. Lewers, M. Abdelhack,
A. Ramasubramanian, J.F. Michael Alphonse, V. Ung, S. El-Gebali, C. Currin, E.
Plomp, R. Thompson, M. Sharan, PLOS Computational Biology 20 (2024).
date_created: 2024-04-02T11:37:32Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-09-04T13:24:19Z
day: '01'
ddc:
- '000'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1011797
external_id:
isi:
- '001181690200005'
pmid:
- '38427633'
file:
- access_level: open_access
checksum: 1f0f837c5b4341f54f6347370ed8c1b7
content_type: application/pdf
creator: dernst
date_created: 2024-04-03T13:29:36Z
date_updated: 2024-04-03T13:29:36Z
file_id: '15289'
file_name: 2024_PloS_Hall.pdf
file_size: 858521
relation: main_file
success: 1
file_date_updated: 2024-04-03T13:29:36Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ten simple rules for pushing boundaries of inclusion at academic events
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: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_type: gold
_id: '15295'
abstract:
- lang: eng
text: "Background: Benzodiazepines and antidepressants are effective agents for
the treatment of generalized anxiety disorder (GAD), with the HAM-A frequently
used as a primary outcome measure. The GAD literature is inconsistent regarding
which medications are more effective for somatic versus psychic symptoms of GAD,
and treatment guidelines do not advocate for prescribing based on subtype. This
meta-analysis aimed to determine whether benzodiazepines and antidepressants have
a differential impact on the somatic versus psychic subscales of the HAM-A in
GAD.\r\n\r\nMethods: An electronic search was undertaken for randomized controlled
trials of either benzodiazepines or antidepressants for GAD that reported treatment
response using the HAM-A subscales. Data were extracted by independent reviewers.
A random effects assessment of weighted mean difference with 95% confidence intervals
and subgroup difference was applied. All analysis was done on SPSS 26. An assessment
of bias, and of quality of evidence was performed.\r\n\r\nResults: 24 randomized
controlled trials met the inclusion criteria: 18 antidepressant trials, 5 benzodiazepine
trials and 1 of both. 14 studies were assessed as having between some and high
risk of bias, while 10 were assessed as having low risk of bias. Benzodiazepines
(WMD of 1.81 [CI 1.03, 2.58]) were significantly more effective than antidepressants
(WMD of 0.83 [CI 0.64, 1.02]) for reducing somatic symptoms of GAD (Chi2 = 5.81,
p = 0.02), and were also more effective (WMD of 2.46 [CI 1.83, 3.09]) in reducing
psychic symptoms than antidepressants (WMD of 1.83 [CI 1.55, 2.10]), although
this comparison did not reach statistical significance (Chi2 = 3.31, p = 0.07).\r\n\r\nConclusion:
The finding that benzodiazepines were significantly more effective than antidepressants
for somatic symptoms needs to be weighed up against potential benefits of antidepressants
over benzodiazepines. It may be useful for future treatment guidelines for GAD
to explicitly consider symptom subtype."
article_number: '152479'
article_processing_charge: Yes
article_type: original
author:
- first_name: Chad
full_name: Beyer, Chad
last_name: Beyer
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Taryn
full_name: Williams, Taryn
last_name: Williams
- first_name: Dan J.
full_name: Stein, Dan J.
last_name: Stein
citation:
ama: Beyer C, Currin C, Williams T, Stein DJ. Meta-analysis of the comparative efficacy
of benzodiazepines and antidepressants for psychic versus somatic symptoms of
generalized anxiety disorder. Comprehensive Psychiatry. 2024;132. doi:10.1016/j.comppsych.2024.152479
apa: Beyer, C., Currin, C., Williams, T., & Stein, D. J. (2024). Meta-analysis
of the comparative efficacy of benzodiazepines and antidepressants for psychic
versus somatic symptoms of generalized anxiety disorder. Comprehensive Psychiatry.
Elsevier. https://doi.org/10.1016/j.comppsych.2024.152479
chicago: Beyer, Chad, Christopher Currin, Taryn Williams, and Dan J. Stein. “Meta-Analysis
of the Comparative Efficacy of Benzodiazepines and Antidepressants for Psychic
versus Somatic Symptoms of Generalized Anxiety Disorder.” Comprehensive Psychiatry.
Elsevier, 2024. https://doi.org/10.1016/j.comppsych.2024.152479.
ieee: C. Beyer, C. Currin, T. Williams, and D. J. Stein, “Meta-analysis of the comparative
efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms
of generalized anxiety disorder,” Comprehensive Psychiatry, vol. 132. Elsevier,
2024.
ista: Beyer C, Currin C, Williams T, Stein DJ. 2024. Meta-analysis of the comparative
efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms
of generalized anxiety disorder. Comprehensive Psychiatry. 132, 152479.
mla: Beyer, Chad, et al. “Meta-Analysis of the Comparative Efficacy of Benzodiazepines
and Antidepressants for Psychic versus Somatic Symptoms of Generalized Anxiety
Disorder.” Comprehensive Psychiatry, vol. 132, 152479, Elsevier, 2024,
doi:10.1016/j.comppsych.2024.152479.
short: C. Beyer, C. Currin, T. Williams, D.J. Stein, Comprehensive Psychiatry 132
(2024).
date_created: 2024-04-07T22:00:55Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-04T13:30:08Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.comppsych.2024.152479
external_id:
isi:
- '001221136000001'
pmid:
- '38564872'
file:
- access_level: open_access
checksum: aadb57448b5f170761ed72cbcc31ba16
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T10:47:20Z
date_updated: 2025-01-13T10:47:20Z
file_id: '18839'
file_name: 2024_ComprehensivePsychiatry_Beyer.pdf
file_size: 2874425
relation: main_file
success: 1
file_date_updated: 2025-01-13T10:47:20Z
has_accepted_license: '1'
intvolume: ' 132'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Comprehensive Psychiatry
publication_identifier:
eissn:
- 1532-8384
issn:
- 0010-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants
for psychic versus somatic symptoms of generalized anxiety disorder
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 132
year: '2024'
...
---
_id: '17092'
abstract:
- lang: eng
text: Memories are thought to be stored in neural ensembles known as engrams that
are specifically reactivated during memory recall. Recent studies have found that
memory engrams of two events that happened close in time tend to overlap in the
hippocampus and the amygdala, and these overlaps have been shown to support memory
linking. It has been hypothesized that engram overlaps arise from the mechanisms
that regulate memory allocation itself, involving neural excitability, but the
exact process remains unclear. Indeed, most theoretical studies focus on synaptic
plasticity and little is known about the role of intrinsic plasticity, which could
be mediated by neural excitability and serve as a complementary mechanism for
forming memory engrams. Here, we developed a rate-based recurrent neural network
that includes both synaptic plasticity and neural excitability. We obtained structural
and functional overlap of memory engrams for contexts that are presented close
in time, consistent with experimental and computational studies. We then investigated
the role of excitability in memory allocation at the network level and unveiled
competitive mechanisms driven by inhibition. This work suggests mechanisms underlying
the role of intrinsic excitability in memory allocation and linking, and yields
predictions regarding the formation and the overlap of memory engrams.
acknowledgement: We thank Sadra Sadeh and Inês Completo Guerreiro for helpful comments
on the manuscript, Yosif Zaki and Denise J. Cai for useful feedback and members
of the Clopath lab for discussion and support. This work was supported by Biotechnology
and Biological Sciences Research Council (BB/N013956/1 awarded to C.C.), Wellcome
Trust (200790/Z/16/Z awarded to C.C.), the Simons Foundation (564408 awarded to
C.C.), and Engineering and Physical Sciences Research Council (EP/R035806/1 awarded
to C.C.).
article_number: e0846232024
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Geoffroy
full_name: Delamare, Geoffroy
last_name: Delamare
- first_name: Douglas
full_name: Feitosa Tomé, Douglas
id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2
last_name: Feitosa Tomé
- first_name: Claudia
full_name: Clopath, Claudia
last_name: Clopath
citation:
ama: Delamare G, Feitosa Tomé D, Clopath C. Intrinsic neural excitability biases
allocation and overlap of memory engrams. Journal of Neuroscience. 2024;44(21).
doi:10.1523/JNEUROSCI.0846-23.2024
apa: Delamare, G., Feitosa Tomé, D., & Clopath, C. (2024). Intrinsic neural
excitability biases allocation and overlap of memory engrams. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0846-23.2024
chicago: Delamare, Geoffroy, Douglas Feitosa Tomé, and Claudia Clopath. “Intrinsic
Neural Excitability Biases Allocation and Overlap of Memory Engrams.” Journal
of Neuroscience. Society for Neuroscience, 2024. https://doi.org/10.1523/JNEUROSCI.0846-23.2024.
ieee: G. Delamare, D. Feitosa Tomé, and C. Clopath, “Intrinsic neural excitability
biases allocation and overlap of memory engrams,” Journal of Neuroscience,
vol. 44, no. 21. Society for Neuroscience, 2024.
ista: Delamare G, Feitosa Tomé D, Clopath C. 2024. Intrinsic neural excitability
biases allocation and overlap of memory engrams. Journal of Neuroscience. 44(21),
e0846232024.
mla: Delamare, Geoffroy, et al. “Intrinsic Neural Excitability Biases Allocation
and Overlap of Memory Engrams.” Journal of Neuroscience, vol. 44, no. 21,
e0846232024, Society for Neuroscience, 2024, doi:10.1523/JNEUROSCI.0846-23.2024.
short: G. Delamare, D. Feitosa Tomé, C. Clopath, Journal of Neuroscience 44 (2024).
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-22T00:00:00Z
date_updated: 2025-09-08T07:40:58Z
day: '22'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0846-23.2024
external_id:
isi:
- '001249681000008'
pmid:
- '38561228'
file:
- access_level: open_access
checksum: 4e19159800db605b802c721e4d4b1ffe
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T06:34:21Z
date_updated: 2024-06-03T06:34:21Z
file_id: '17095'
file_name: 2024_JourNeuroscience_Delamare.pdf
file_size: 920354
relation: main_file
success: 1
file_date_updated: 2024-06-03T06:34:21Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intrinsic neural excitability biases allocation and overlap of memory engrams
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: 44
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '19520'
abstract:
- lang: eng
text: Vertebrates exhibit a wide range of motor behaviors, ranging from swimming
to complex limb-based movements. Here we take advantage of frog metamorphosis,
which captures a swim-to-limb-based movement transformation during the development
of a single organism, to explore changes in the underlying spinal circuits. We
find that the tadpole spinal cord contains small and largely homogeneous populations
of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages.
These neuronal populations only modestly increase in number and subtype heterogeneity
with the emergence of free swimming. In contrast, during frog metamorphosis and
the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron
number and transcriptional heterogeneity, culminating in cohorts of neurons that
exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated
gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively,
results in severe but selective deficits in tail and limb function. Our work thus
demonstrates that neural diversity scales exponentially with increasing behavioral
complexity and illustrates striking evolutionary conservation in the molecular
organization and function of motor circuits across species.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We would like to thank the members of the Sweeney Lab (especially
Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project
and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion,
and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their
scientific insight and mentorship during the conception of this project. This\r\nproject
would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena
Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA).
In addition, we thank our funding sources for providing the resources to do these\r\nexperiments:
FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon
Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch
Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS
5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.);
NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities
(ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472
(Z.H.); and Project A.L.S. (S.B-M.). "
article_processing_charge: No
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
- first_name: 'Florina Alexandra '
full_name: 'Toma, Florina Alexandra '
id: 2f73f876-f128-11eb-9611-b96b5a30cb0e
last_name: Toma
- first_name: Zoe P
full_name: Harrington, Zoe P
id: a8144562-32c9-11ee-b5ce-d9800628bda2
last_name: Harrington
orcid: 0009-0008-0158-4032
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Alexandra J.
full_name: Trevisan, Alexandra J.
last_name: Trevisan
- first_name: Phillip
full_name: Chapman, Phillip
last_name: Chapman
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales
exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv.
doi:10.1101/2024.09.20.614050
apa: Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R.,
Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially
with swim-to-limb transformation during frog metamorphosis. bioRxiv. https://doi.org/10.1101/2024.09.20.614050
chicago: Vijatovic, David, Florina Alexandra Toma, Zoe P Harrington, Christoph
M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal
Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during
Frog Metamorphosis.” BioRxiv, n.d. https://doi.org/10.1101/2024.09.20.614050.
ieee: D. Vijatovic et al., “Spinal neuron diversity scales exponentially
with swim-to-limb transformation during frog metamorphosis,” bioRxiv. .
ista: Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ,
Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney
LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation
during frog metamorphosis. bioRxiv, 10.1101/2024.09.20.614050.
mla: Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with
Swim-to-Limb Transformation during Frog Metamorphosis.” BioRxiv, doi:10.1101/2024.09.20.614050.
short: D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J.
Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen,
J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.).
corr_author: '1'
date_created: 2025-04-07T08:48:28Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2025-05-14T11:40:13Z
day: '27'
department:
- _id: LoSw
- _id: TiVo
- _id: Bio
- _id: NiBa
doi: 10.1101/2024.09.20.614050
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.09.20.614050
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473
grant_number: CZI01
name: Tools for automation and feedback microscopy
publication: bioRxiv
publication_status: submitted
status: public
title: Spinal neuron diversity scales exponentially with swim-to-limb transformation
during frog metamorphosis
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17886'
abstract:
- lang: eng
text: 'Thin pancake-like neuronal networks cultured on top of a planar microelectrode
array have been extensively tried out in neuroengineering, as a substrate for
the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts
failed due to intricate self-organizing dynamics in the neuronal systems. In particular,
the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”)
of spontaneous population spikes. Being unpredictable and independent of the surface
electrode locations, the n-sites drastically change local ability of the network
to generate spikes. Here, using a spiking neuronal network model with generative
spatially-embedded connectome, we systematically show in simulations that the
number, location, and relative activity of spontaneously formed n-sites (“the
vitals”) crucially depend on the samplings of three distributions: (1) the network
distribution of neuronal excitability, (2) the distribution of connections between
neurons of the network, and (3) the distribution of maximal amplitudes of a single
synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about
4%) of non-pacemaker neurons having the highest excitability was enough to completely
suppress the occurrence of population spikes and their n-sites. This key result
is explained theoretically. Remarkably, the n-sites occur taking into account
only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity.
As the spiking network model used in this study is strictly deterministic, all
simulation results can be accurately reproduced. The model, which has already
demonstrated a very high richness-to-complexity ratio, can also be directly extended
into the three-dimensional case, e.g., for targeting peculiarities of spiking
dynamics in cerebral (or brain) organoids. We recommend the model as an excellent
illustrative tool for teaching network-level computational neuroscience, complementing
a few benchmark models.'
acknowledgement: A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and
Tim P. Vogels for useful discussions. This work was supported by a European Research
Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels).
article_number: '106589'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dmitrii
full_name: Zendrikov, Dmitrii
last_name: Zendrikov
- first_name: Alexander
full_name: Paraskevov, Alexander
id: d05e3c56-9262-11ed-9231-be692464e5ac
last_name: Paraskevov
citation:
ama: Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous
spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks.
2024;180. doi:10.1016/j.neunet.2024.106589
apa: Zendrikov, D., & Paraskevov, A. (2024). The vitals for steady nucleation
maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks.
Neural Networks. Elsevier. https://doi.org/10.1016/j.neunet.2024.106589
chicago: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation
Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.”
Neural Networks. Elsevier, 2024. https://doi.org/10.1016/j.neunet.2024.106589.
ieee: D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of
spontaneous spiking coherence in autonomous two-dimensional neuronal networks,”
Neural Networks, vol. 180. Elsevier, 2024.
ista: Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of
spontaneous spiking coherence in autonomous two-dimensional neuronal networks.
Neural Networks. 180, 106589.
mla: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation
Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.”
Neural Networks, vol. 180, 106589, Elsevier, 2024, doi:10.1016/j.neunet.2024.106589.
short: D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024).
corr_author: '1'
date_created: 2024-09-08T22:01:10Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-08T09:12:20Z
day: '01'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1016/j.neunet.2024.106589
ec_funded: 1
external_id:
isi:
- '001316474600001'
pmid:
- '39217864'
file:
- access_level: open_access
checksum: 6a194323234e01d4ae725f674529cdb1
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T08:26:08Z
date_updated: 2025-01-13T08:26:08Z
file_id: '18825'
file_name: 2024_NeuralNetworks_Zendrikov.pdf
file_size: 6162281
relation: main_file
success: 1
file_date_updated: 2025-01-13T08:26:08Z
has_accepted_license: '1'
intvolume: ' 180'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Neural Networks
publication_identifier:
eissn:
- 1879-2782
issn:
- 0893-6080
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous
two-dimensional neuronal networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 180
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15169'
abstract:
- lang: eng
text: Interpretation of extracellular recordings can be challenging due to the long
range of electric field. This challenge can be mitigated by estimating the current
source density (CSD). Here we introduce kCSD-python, an open Python package implementing
Kernel Current Source Density (kCSD) method and related tools to facilitate CSD
analysis of experimental data and the interpretation of results. We show how to
counter the limitations imposed by noise and assumptions in the method itself.
kCSD-python allows CSD estimation for an arbitrary distribution of electrodes
in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in
a single cell, and includes a range of diagnostic aids. We demonstrate its features
in a Jupyter Notebook tutorial which illustrates a typical analytical workflow
and main functionalities useful in validating analysis results.
acknowledgement: 'The Python implementation of kCSD was started by Grzegorz Parka
during Google Summer of Code project through the International Neuroinformatics
Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class.
This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691
to DKW; 2015/17/B/ST7/04123 to DKW). '
article_number: e1011941
article_processing_charge: Yes
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Marta
full_name: Bejtka, Marta
last_name: Bejtka
- first_name: Wladyslaw
full_name: Sredniawa, Wladyslaw
last_name: Sredniawa
- first_name: Michal
full_name: Czerwinski, Michal
last_name: Czerwinski
- first_name: Jakub M.
full_name: Dzik, Jakub M.
last_name: Dzik
- first_name: Joanna
full_name: Jedrzejewska-Szmek, Joanna
last_name: Jedrzejewska-Szmek
- first_name: Daniel K.
full_name: Wojciki, Daniel K.
last_name: Wojciki
citation:
ama: Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source
density estimation with quality control. PLoS Computational Biology. 2024;20(3).
doi:10.1371/journal.pcbi.1011941
apa: Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek,
J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density
estimation with quality control. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1011941
chicago: Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski,
Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python,
Reliable Current Source Density Estimation with Quality Control.” PLoS Computational
Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941.
ieee: C. Chintaluri et al., “kCSD-python, reliable current source density
estimation with quality control,” PLoS Computational Biology, vol. 20,
no. 3. Public Library of Science, 2024.
ista: Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek
J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with
quality control. PLoS Computational Biology. 20(3), e1011941.
mla: Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density
Estimation with Quality Control.” PLoS Computational Biology, vol. 20,
no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941.
short: C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek,
D.K. Wojciki, PLoS Computational Biology 20 (2024).
corr_author: '1'
das_tickbox: '1'
date_created: 2024-03-24T23:00:59Z
date_published: 2024-03-14T00:00:00Z
date_updated: 2026-07-13T12:30:33Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1011941
external_id:
isi:
- '001190689800001'
pmid:
- '38484020'
file:
- access_level: open_access
checksum: c09718d0d09614642d877d0716ce32e8
content_type: application/pdf
creator: dernst
date_created: 2025-06-25T05:47:36Z
date_updated: 2025-06-25T05:47:36Z
file_id: '19897'
file_name: 2024_PLoSCompBio_Chintaluri.pdf
file_size: 2540277
relation: main_file
success: 1
file_date_updated: 2025-06-25T05:47:36Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
eissn:
- 1553-7358
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Neuroinflab/kCSD-python
scopus_import: '1'
status: public
title: kCSD-python, reliable current source density estimation with quality control
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: 20
year: '2024'
...