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Astrocyte-mediated higher-order control of synaptic plasticity.

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  1. [1] § Methods › Dimension two dynamics: the astrocytes ↔ AstroCircuit_Functions.jl, lines 92–130 · score 0.61 · exponential decay, calcium pumps, neighbors, DCa, networks, dynamics

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The authors' code

Julia · 199 lines · 5.3 KB · CC-BY-4.0 · 1 match

  1. using Graphs, Distributions, Plots, GraphRecipes, LaTeXStrings, Random
  3. function GaussianFluc(Mean,Std,NN,T)
  5. d = Normal(0,Std)
  7. return Mean .+ rand(d,T,NN)
  8. end
  10. rg1 = Random.seed!(123)
  12. function Steady_randAmpl(a,b,NN)
  13. return (a .+ rand(rg1,NN).*(b-a)) # nA
  14. end
  16. function PoissonStim(f,T,NN)
  18. spkT = zeros(T,NN);
  20. for t in 1:T
  22. spkT[t,:] = 1 .*(rand(NN).<(f./1000)*dt)
  24. end
  26. return spkT
  27. end
  29. function PeriodicStim(f,Df,NN,T,ini,ifi)
  31. isi = Int.(round.((1000 ./f)/dt)) #inter spke interval ms
  33. spkT = zeros(T,NN);
  35. for t in ini:ifi
  37. spkT[t,:] = ((t .- Df) .% isi) .== 0
  39. end
  41. return spkT
  42. end
  44. function SimAstroNet!(filename,AN,AL,AG,spkiT,IT,T,VT,xT,yT,yiT,UT,gamasT,gampreT,IP3T,CaT,xaT,GlioRel,V,x,xa,IP3,Ca,y,yi,tsp,tspa,spk,U,gamas,gampre,USE,Grel,th1,th2,dts,params,Heavi=false,spkT=[0])
  46. filename1 = filename*"_spk.txt"
  48. io1 = open(filename1,"w")
  50. Use,Usa,eps,alph = params
  52. # Initialize
  53. V .*= 0.
  54. x .= 1.
  55. xa .= 1.
  56. IP3 .*= 0.
  57. Ca .*= 0.
  58. y .*= 0.
  59. yi .*= 0.
  60. gamas .*= 0.
  61. gampre .*= 0.
  63. # Initialize U
  64. U[:,:] = Use.*AN;
  65. #USE is a matrix, just in case we want long-term plasticity effects or heterogeinity in the steady state of u
  66. USE[:,:] = Use.*AN;
  67. VT[1,:] .= V
  68. yiT[1,:] .= 0.
  69. yT[1,:,:] .= 0.
  70. xT[1,:,:] .= x
  71. UT[1,:,:] .= U
  72. gamasT[1,:,:] .= 0
  73. gampreT[1,:,:] .= 0
  74. IP3T[1,:,:] .= IP3
  75. CaT[1,:] .= Ca
  76. xaT[1,:,:] .= xa;
  78. spkiT .*= 0
  79. tsp .*= 0
  80. tspa .*= 0
  81. spk .*= 0
  83. ttas = tas/dt
  85. coss = length(spkT)
  87. for t in 2:T
  89. # NEURONS DYNAMICS: during absolute retractory period, V is hyperpolarized
  90. V .+= ((t.-tsp).>(ta/dt)).*dt.*(-V .+ R.*(IT .+ ame.*yi .+ am.*reduce(+,y,dims=1)'))./tauV
  92. # If we have external spikes coming to the network
  93. if coss>1
  94. yi .+= dt.*(-yi./tausin) .+ spkT[t,:]
  95. else
  96. yi .= 0
  97. end
  99. y .+= dt.*(-y./tausin) .+ U.*alph.*x.*spk
  101. # Save the current propagated to neighbors after a spike
  102. if sum(spk)!=0
  104. id = findall(e->e==1,spk)
  106. for ni in id
  108. writedlm(io1,reduce(hcat, [ni,round(t*dt,digits=4),round(y[SyIndx[Isy[ni]]],digits=5),round(U[SyIndx[Isy[ni]]],digits=5),round(x[SyIndx[Isy[ni]]],digits=5),V[Isy[ni]],dt.*(t.-tsp[Isy[ni]])]))
  110. end
  111. end
  113. # If we want crossing threshold case, we should evaluate th1 before and after
  114. #th1 = (Ca.<Cathr)
  116. # With calcium pump
  117. # Ca .+= dt.*( -Cs.*(Ca.^2)./(Ks.^2 .+(Ca.^2)) .+ beta.*reduce(+,IP3',dims=2) .+ Dca.*reduce(+,AG.*(Ca' .- Ca),dims=2))
  119. # With calcium exponential decay
  120. Ca .+= dt.*(-Ca./tauCa .+ beta.*reduce(+,IP3',dims=2) .+ Dca.*reduce(+,AG.*(Ca' .- Ca),dims=2))
  122. # ASTROCYTE DYNAMICS
  123. IP3 .+= dt.*( -IP3./tauIP3 ) .+ (1-alph).*(AL.*((U.*spk.*x)[SyIndx])).*(1 .-IP3)
  125. # DEPRESSION
  126. # Neuro-depression
  127. x .+= dt.*(1 .- x)./taur - U.*x.*spk
  129. # FACILITATION DYNAMICS
  130. U .= USE .+ (eps .- USE).*gamas .+ (1 .- USE).*gampre
  132. # Activation fraction via presynaptic mechanism
  133. gamas[SyIndx] .+= -dt.*gamas[SyIndx]/tau2f + reduce(+,(AL.*xa.*Usa) .* Grel',dims=2).*(1. .-(gampre[SyIndx].+gamas[SyIndx]))
  135. # Activation fraction via presynaptic mechanism
  136. gampre .+= -dt.*gampre/tau1f + USE.*(1 .-(gamas.+gampre)).*spk
  138. # Glio-depression
  139. xa .+= dt.*(1 .-xa)./taura .- (AL.*xa.*Usa) .* Grel'
  141. ###################################################
  142. #Effects that will take place in the next timestep
  143. ###################################################
  145. # To save last spike time
  146. tsp .= tsp.*(spk.==0) .+ t.*(spk.==1)
  148. # To fire or not fire
  149. spk .= (V .> thrs).*((t.-tsp).>(ta/dt))
  151. # To indicate spikes I include a peak before reset (Optional)
  152. #V .+= spk.*60
  154. if Heavi==false #Will use the consecutive release event each tas
  155. # To save last glio.release time
  156. tspa .= tspa.*(Grel.==0) .+ t.*(Grel.==1)
  158. # If time elapsed after last glio.release is greater than tas
  159. th1 .= (t.-tspa).> ttas
  160. else
  161. th1 .= 1
  162. end
  164. # And calcium above threshold
  165. th2 .= (Ca.>Cathr)
  167. # In the discontinuity, we don't multiply by the integration step,
  168. # But after it, we should multiplied by dt
  169. Grel .= th1.*th2.*(dt.*(Grel.>0) .+ (Grel.==0))
  171. spkiT[t,:] .= spk
  173. if t%dts ==0
  175. tt = Int32(t/dts)
  177. VT[tt,:] .= V
  178. yiT[tt,:] .= yi .+ IT
  179. xT[tt,:,:] .= x
  180. yT[tt,:,:] .= y
  181. UT[tt,:,:] .= U
  182. gamasT[tt,:,:] .= gamas
  183. gampreT[tt,:,:] .= gampre
  184. IP3T[tt,:,:] .= IP3
  185. CaT[tt,:] .= Ca
  186. xaT[tt,:,:] .= xa
  187. GlioRel[tt,:,:] .= Grel
  189. end
  191. # Reset because spike occurs
  192. V .= V.*(1 .-spk) .+ Vreset .*spk;
  194. end
  196. close(io1)
  198. return nothing
  199. end

AstroCircuit_Functions.jl, under CC-BY-4.0 · at the source

Overview

Authors: Gustavo Menesse1,2, Ana P. Millán1, Joaquín J. Torres1
ORCID iDs: Ana P. Millán, Joaquín J. Torres
  1. Department of Electromagnetism and Matter Physics and Institute “Carlos I” of Theoretical and Computational Physics, University of Granada,Granada, Spain
  2. Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Asunción,San Lorenzo, Paraguay
Institutions: Universidad de Granada (Spain); Universidad Nacional de Asunción (Paraguay)
Journal: Communications biology, volume 9, issue 1, article 684
Dates: received 25 July 2025; accepted 31 March 2026; published online 13 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-10044-y · PMID 41975021 · PMCID PMC13190846 · OpenAlex W4416289346
Open access: gold, a free copy (OpenAlex)
Preprint: arxiv:2507.07693
Status: code verified
Categories: computational modeling (no new data) (modality), none (in silico) (organism), cellular / molecular (subfield)
Keywords: Network models, Biophysical models, Computational biophysics
MeSH: Astrocytes*, Models, Neurological*, Neuronal Plasticity*, Neurons*, Synapses*, Animals, Synaptic Transmission (* major topic)
Topic: Neuroscience and Neuropharmacology Research (Cellular and Molecular Neuroscience, Neuroscience), according to OpenAlex
Funding: Work supported by Grant No. PID2023-149174NB-I00 financed by the Spanish Ministry and Agencia Estatal de Investigación MICIU/AEI/10.13039/501100011033 and ERDF funds (European Union); ``Programa Nacional de Becas de Postgrados en el Exterior “Don Carlos Antonio López” - BECAL” of the Ministry of Economy and Finance of Paraguay; Work supported by Grant No. PID2023-149174NB-I00 financed by the Spanish Ministry and Agencia Estatal de Investigación MICIU/AEI/10.13039/501100011033 and ERDF funds (European Union) and by 'Ramón y Cajal' program of the Spanish Ministry of Science and Innovation (Grant RYC2021-031241-I)
Citations: cited by 1 paper (Europe PMC); 98 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

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Zenodo 19260114

License: CC-BY-4.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Languages: Jupyter (1), Julia (1)
Size: 2 files, 2 scripts
Software Heritage: not checked
Found in: the references
Holds: 1 notebook
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Distributions.jl (1 file), Plots.jl (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
  • 29 September 2026: the link answers (HTTP 200)
1 file
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Read it in the paper: doi.org/10.1038/s42003-026-10044-y.

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 3 keywords, 7 MeSH terms, 3 funders, 90 references.

Cite

This paper

Menesse, G., Millán, A. P., & Torres, J. J. (2026). Astrocyte-mediated higher-order control of synaptic plasticity. Communications biology, 9(1), 684. https://doi.org/10.1038/s42003-026-10044-y

BibTeX

@article{menesse2026astrocyte,
author = {Menesse, Gustavo and Millán, Ana P. and Torres, Joaquín J.},
title = {{Astrocyte-mediated higher-order control of synaptic plasticity}},
journal = {Communications biology},
year = {2026},
month = apr,
volume = {9},
number = {1},
pages = {684},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10044-y},
url = {https://doi.org/10.1038/s42003-026-10044-y},
pmid = {41975021},
pmcid = {PMC13190846}
}

RIS

TY - JOUR
AU - Menesse, Gustavo
AU - Millán, Ana P.
AU - Torres, Joaquín J.
TI - Astrocyte-mediated higher-order control of synaptic plasticity
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/04/13
VL - 9
IS - 1
SP - 684
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10044-y
UR - https://doi.org/10.1038/s42003-026-10044-y
LA - en
ER -

CSL-JSON

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],
"container-title-short": "Commun Biol",
"volume": "9",
"issue": "1",
"page": "684",
"DOI": "10.1038/s42003-026-10044-y",
"PMID": "41975021",
"PMCID": "PMC13190846",
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