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Human cortex organizes dynamic co-fluctuations along the sensorimotor-association axis.

Code ↔ Paper

17 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 17 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Results › Amplitude-dependent spatial configuration of co-fluctuation scores along the SA axis ↔ scripts/testing_phase_random.m, lines 82–144 · score 0.79 · 50–55 %, 75–80 %, SA axis, shifts, maps, bins
  2. [2] § Results › Amplitude-dependent spatial configuration of co-fluctuation scores along the SA axis ↔ scripts/testing_individual_analysis.m, lines 128–172 · score 0.79 · 50–55 %, 75–80 %, SA axis, maps, score, bins
  3. [3] § Methods › Delineating the changes of co-fluctuation scores across global amplitudes ↔ scripts/fitGAMs_CS_Schaefer200x17.R, lines 1–70 · score 0.75 · tSNR, smooth term, co fluctuation amplitude, regional co fluctuation, co fluctuation score, maximal
  4. [4] § Methods › Delineating the changes of co-fluctuation scores across global amplitudes ↔ scripts/GAMs_fixed.R, lines 22–151 · score 0.74 · GAM smooth term, reduced model, smooth function, nested, curvature, ANOVA
  5. [5] § Methods › MRI acquisition ↔ H3/DREAM/D_core/fsio/ssbloch.m, the whole file · a weak match · score 0.73 · echo planar imaging, flip angle, coil, sequence, resolution, TE
  6. [6] § Methods › Delineating the changes of co-fluctuation scores across global amplitudes ↔ scripts/GAMs_mixed.R, lines 17–128 · score 0.72 · GAM smooth term, reduced model, smooth function, nested, ANOVA, derivatives
  7. [7] § Methods › Delineating the changes of co-fluctuation scores across global amplitudes ↔ scripts/GAMs_fixed.R, lines 22–151 · score 0.68 · tSNR, smooth term, AIC, REML, maximal, sex
  8. [8] § Results › Developmental refinement of opposing co-fluctuation patterns along the SA axis ↔ scripts/testing_hcpd_cs.m, lines 139–193 · score 0.66 · 90–100 %, SA axis, 60 %, 40 %, age, scores
  9. [9] § Methods › MRI data preprocessing ↔ H3/DREAM/D_core/fsio/ssbloch.m, the whole file · a weak match · score 0.65 · high resolution T1, magnetic field, CSF
  10. [10] § Results › Sensitivity and replication analyses ↔ scripts/fit_GAMs_fixed_glasser360_3T.R, lines 1–59 · score 0.61 · head motion, global signal, tSNR, co fluctuation scores, covariate, GS
  11. [11] § Results › Sensitivity and replication analyses ↔ scripts/fit_GAMs_fixed_schaefer400x17_3T.R, lines 1–59 · score 0.61 · head motion, global signal, tSNR, co fluctuation scores, covariate, GS
  12. [12] § Methods › MRI data preprocessing ↔ H1/ccs_04_funcAROMA.sh, the whole file · a weak match · score 0.57 · ICA AROMA, fMRI, nuisance, motion, CCS, smoothing
  13. [13] § Methods › MRI data preprocessing ↔ samplesScripts/ccs_funcproc_template.sh, lines 47–129 · score 0.56 · band pass filtered, detrended, preprocessed, surface, regressed, space
  14. [14] § Methods › MRI data preprocessing ↔ H1/ccs_05_funcpreproc_cortex.sh, lines 54–128 · score 0.54 · band pass filtered, detrended, cortex, surface, linearly, MRI
  15. [15] § Results ↔ scripts/ets_rss_physio_phase_mapping.m, the whole file · a weak match · score 0.53 · heart rate, global RSS, unwrapped, root, frame, signals
  16. [16] § Results ↔ bins_hcp_co_fluc_analysis.m, lines 36–102 · score 0.52 · Static FC, global RSS, timeseries, HCP, co fluctuation, Connectome
  17. [17] § Methods › MRI data preprocessing ↔ scripts/ets_rss_physio_phase_mapping.m, the whole file · a weak match · score 0.51 · heart rate, physiological, HRV, interval, windows, MRI

Paper

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The authors' code

R · 228 lines · 11 KB · no license · 2 matches

  1. library(dplyr)
  2. library(R.matlab)
  3. library(ggsegGlasser)
  4. library(ggsegSchaefer)
  5. library(ggseg)
  6. library(ggplot2)
  7. library(ggseg3d)
  8. library(cifti)
  9. library(stringr)
  10. library(factoextra)
  11. library(matrixStats)
  12. library(scales)
  13. library(Hmisc)
  14. library(tidyr)
  15. library(cocor)
  16. library(mgcv)
  17. library(gratia)
  18. library(tidyverse)
  19. library(numDeriv)
  20. #### FIT GAM SMOOTH ####
  21. ## Function to fit a GAM (measure ~ s(smooth_var, k = knots, fx = set_fx) + covariates)).
  22. ## measure:cs
  23. ## region: V1...
  24. ## smooth_var: bin_label
  25. ## covariates: sex + age + tSNR + mean_fd + mean_gs + mean_hr + mean_br
  26. ## knots: 3
  27. ## set_fx = TRUE
  28. ## stats_only = FALSE
  29. gam.fit.smooth <- function(region, smooth_var, covariates, knots, set_fx = FALSE, stats_only = FALSE){
  30. # compatible settings.
  31. parcel <- region
  32. #Fit the gam
  33. modelformula <- as.formula(sprintf("%s ~ s(%s, k = %s, fx = %s) + %s", region, smooth_var, knots, set_fx, covariates))
  34. gam.model <- gam(modelformula, method = "REML", data = gam.data)
  35. gam.results <- summary(gam.model)
  36. summary(gam.model)
  37. p.pv <- gam.results$p.pv
  38. p.t <- gam.results$p.t
  39. gam_check_k <- k.check(gam.model)
  40. aic_values <- AIC(gam.model)
  41. # browser()
  42. #GAM derivatives
  43. #Get derivatives of the smooth function using finite differences
  44. derv <- derivatives(gam.model, term = sprintf('s(%s)',smooth_var), interval = "simultaneous", unconditional = F) #derivative at 200 indices of smooth_var with a simultaneous CI
  45. #Identify derivative significance window(s)
  46. derv <- derv %>% #add "sig" column (TRUE/FALSE) to derv
  47. mutate(sig = !(0 > lower & 0 < upper)) #derivative is sig if the lower CI is not < 0 while the upper CI is > 0 (i.e., when the CI does not include 0)
  48. derv$sig_deriv = derv$derivative*derv$sig #add "sig_deriv derivatives column where non-significant derivatives are set to 0
  49. # second derivatives
  50. derv2l <- derivatives(gam.model, term = sprintf('s(%s)',smooth_var), order = 2)
  51. mean.derivative_2l <- mean(derv2l$derivative)
  52. # first derivatives
  53. derv1l <- derivatives(gam.model, term = sprintf('s(%s)',smooth_var), order = 1)
  54. # curvature.
  55. d1 <- derv1l$derivative
  56. d2 <- derv2l$derivative
  57. curvature <- abs(d2) / (1 + d1^2)^(3/2)
  58. mean.curvature <- mean(curvature)
  59. # print(curvature)
  60. # print(length(curvature))
  61. # print(mean(curvature))
  62. #GAM statistics
  63. #F value for the smooth term and GAM-based significance of the smooth term
  64. gam.smooth.F <- gam.results$s.table[3]
  65. gam.smooth.pvalue <- gam.results$s.table[4]
  66. #Calculate the magnitude and significance of the smooth term effect by comparing full and reduced models
  67. ##Compare a full model GAM (with the smooth term) to a nested, reduced model (with covariates only)
  68. nullmodel <- as.formula(sprintf("%s ~ %s", region, covariates)) #no smooth term
  69. gam.nullmodel <- gam(nullmodel, method = "REML", data = gam.data)
  70. gam.nullmodel.results <- summary(gam.nullmodel)
  71. ##Full versus reduced model anova p-value
  72. anova.smooth.pvalue <- anova.gam(gam.nullmodel,gam.model,test='Chisq')$`Pr(>Chi)`[2]
  73. ##Full versus reduced model direction-dependent partial R squared
  74. ### effect size
  75. sse.model <- sum((gam.model$y - gam.model$fitted.values)^2)
  76. sse.nullmodel <- sum((gam.nullmodel$y - gam.nullmodel$fitted.values)^2)
  77. partialRsq <- (sse.nullmodel - sse.model)/sse.nullmodel
  78. ### effect direction
  79. mean.derivative <- mean(derv$derivative)
  80. if(mean.derivative < 0){ #if the average derivative is less than 0, make the effect size estimate negative
  81. partialRsq <- partialRsq*-1}
  82. #Derivative-based temporal characteristics
  83. #Age of developmental change onset
  84. if(sum(derv$sig) > 0){ #if derivative is significant at at least 1 age
  85. change.onset <- min(derv$data[derv$sig==T])
  86. } #find first age in the smooth where derivative is significant
  87. if(sum(derv$sig) == 0){ #if gam derivative is never significant
  88. change.onset <- NA
  89. } #assign NA
  90. #Age of maximal developmental change
  91. if(sum(derv$sig) > 0){
  92. derv$abs_sig_deriv = round(abs(derv$sig_deriv),5) #absolute value significant derivatives
  93. maxval <- max(derv$abs_sig_deriv) #find the largest derivative
  94. window.peak.change <- derv$data[derv$abs_sig_deriv == maxval] #identify the age(s) at which the derivative is greatest in absolute magnitude
  95. peak.change <- mean(window.peak.change)} #identify the age of peak developmental change
  96. if(sum(derv$sig) == 0){
  97. peak.change <- NA
  98. }
  99. #Age of decrease onset
  100. if(sum(derv$sig) > 0){
  101. decreasing.range <- derv$data[derv$sig_deriv < 0] #identify all ages with a significant negative derivative (i.e., smooth_var indices where y is decreasing)
  102. if(length(decreasing.range) > 0)
  103. decrease.onset <- min(decreasing.range) #find youngest age with a significant negative derivative
  104. if(length(decreasing.range) == 0)
  105. decrease.onset <- NA
  106. }
  107. if(sum(derv$sig) == 0){
  108. decrease.onset <- NA
  109. }
  110. #Age of increase offset
  111. if(sum(derv$sig) > 0){
  112. increasing.range <- derv$data[derv$sig_deriv > 0] #identify all ages with a significant positive derivative (i.e., smooth_var indices where y is increasing)
  113. if(length(increasing.range) > 0)
  114. increase.offset <- max(increasing.range) #find oldest age with a significant positive derivative
  115. if(length(increasing.range) == 0)
  116. increase.offset <- NA
  117. }
  118. if(sum(derv$sig) == 0){
  119. increase.offset <- NA
  120. }
  121. #Age of maturation
  122. if(sum(derv$sig) > 0){
  123. change.offset <- max(derv$data[derv$sig==T])
  124. } #find last age in the smooth where derivative is significant
  125. if(sum(derv$sig) == 0){
  126. change.offset <- NA
  127. }
  128. full.results <- cbind(parcel, gam.smooth.F, gam.smooth.pvalue, partialRsq, anova.smooth.pvalue,
  129. change.onset, peak.change, decrease.onset, increase.offset, change.offset,
  130. mean.curvature, mean.derivative_2l)
  131. stats.results <- cbind(parcel, gam.smooth.F, gam.smooth.pvalue, partialRsq, anova.smooth.pvalue)
  132. if(stats_only == TRUE)
  133. return(list(results=stats.results, p.pv=p.pv, p.t=p.t, gam_check_k=gam_check_k, aic_values=aic_values))
  134. if(stats_only == FALSE)
  135. # return(full.results)
  136. return(list(results=full.results, p.pv=p.pv, p.t=p.t, gam_check_k=gam_check_k, aic_values=aic_values))
  137. }
  138. #### PREDICT GAM SMOOTH FITTED VALUES ####
  139. ## Function to predict fitted values of a measure based on a fitted GAM smooth
  140. ## (measure ~ s(smooth_var, k = knots, fx = set_fx) + covariates)) and a prediction df.
  141. gam.smooth.predict <- function(region, smooth_var, covariates, knots, set_fx = FALSE, increments){
  142. parcel <- region
  143. region <- str_replace(region, "-", ".")
  144. modelformula <- as.formula(sprintf("%s ~ s(%s, k = %s, fx = %s) + %s", region, smooth_var, knots, set_fx, covariates))
  145. gam.model <- gam(modelformula, method = "REML", data = gam.data)
  146. gam.results <- summary(gam.model)
  147. #Extract gam input data
  148. df <- gam.model$model #extract the data used to build the gam, i.e., a df of y + predictor values
  149. #Create a prediction data frame
  150. np <- increments #number of predictions to make; predict at np increments of smooth_var
  151. thisPred <- data.frame(init = rep(0,np)) #initiate a prediction df
  152. theseVars <- attr(gam.model$terms,"term.labels") #gam model predictors (smooth_var + covariates)
  153. varClasses <- attr(gam.model$terms,"dataClasses") #classes of the model predictors and y measure
  154. thisResp <- as.character(gam.model$terms[[2]]) #the measure to predict
  155. for (v in c(1:length(theseVars))) { #fill the prediction df with data for predictions. These data will be used to predict the output measure (y) at np increments of the smooth_var, holding other model terms constant
  156. thisVar <- theseVars[[v]]
  157. thisClass <- varClasses[thisVar]
  158. if (thisVar == smooth_var) {
  159. thisPred[,smooth_var] = seq(min(df[,smooth_var],na.rm = T),max(df[,smooth_var],na.rm = T), length.out = np) #generate a range of np data points, from minimum of smooth term to maximum of smooth term
  160. } else {
  161. switch (thisClass,
  162. "numeric" = {thisPred[,thisVar] = median(df[,thisVar])}, #make predictions based on median value
  163. "factor" = {thisPred[,thisVar] = levels(df[,thisVar])[[1]]}, #make predictions based on first level of factor
  164. "ordered" = {thisPred[,thisVar] = levels(df[,thisVar])[[1]]} #make predictions based on first level of ordinal variable
  165. )
  166. }
  167. }
  168. pred <- thisPred %>% select(-init)
  169. #Generate predictions based on the gam model and predication data frame
  170. predicted.smooth <- fitted_values(object = gam.model, data = pred)
  171. predicted.smooth <- predicted.smooth %>% select(all_of(smooth_var), fitted, se, lower, upper)
  172. smooth.fit <- list(parcel, predicted.smooth)
  173. return(smooth.fit)
  174. }
  175. #### CALCULATE SMOOTH ESTIMATES ####
  176. ## Function to estimate the zero-averaged gam smooth function
  177. gam.estimate.smooth <- function(region, smooth_var, covariates, knots, set_fx = FALSE, increments){
  178. # compatible settings.
  179. parcel <- region
  180. modelformula <- as.formula(sprintf("%s ~ s(%s, k = %s, fx = %s) + %s", region, smooth_var, knots, set_fx, covariates))
  181. gam.model <- gam(modelformula, method = "REML", data = gam.data)
  182. gam.results <- summary(gam.model)
  183. #Extract gam input data
  184. df <- gam.model$model #extract the data used to build the gam, i.e., a df of y + predictor values
  185. #Create a prediction data frame
  186. np <- increments #number of predictions to make; predict at np increments of smooth_var
  187. thisPred <- data.frame(init = rep(0,np)) #initiate a prediction df
  188. theseVars <- attr(gam.model$terms,"term.labels") #gam model predictors (smooth_var + covariates)
  189. varClasses <- attr(gam.model$terms,"dataClasses") #classes of the model predictors and y measure
  190. thisResp <- as.character(gam.model$terms[[2]]) #the measure to predict
  191. for (v in c(1:length(theseVars))) { #fill the prediction df with data for predictions. These data will be used to predict the output measure (y) at np increments of the smooth_var, holding other model terms constant
  192. thisVar <- theseVars[[v]]
  193. thisClass <- varClasses[thisVar]
  194. if (thisVar == smooth_var) {
  195. thisPred[,smooth_var] = seq(min(df[,smooth_var],na.rm = T),max(df[,smooth_var],na.rm = T), length.out = np) #generate a range of np data points, from minimum of smooth term to maximum of smooth term
  196. } else {
  197. switch (thisClass,
  198. "numeric" = {thisPred[,thisVar] = median(df[,thisVar])}, #make predictions based on median value
  199. "factor" = {thisPred[,thisVar] = levels(df[,thisVar])[[1]]}, #make predictions based on first level of factor
  200. "ordered" = {thisPred[,thisVar] = levels(df[,thisVar])[[1]]} #make predictions based on first level of ordinal variable
  201. )
  202. }
  203. }
  204. pred <- thisPred %>% select(-init)
  205. #Estimate the smooth trajectory
  206. estimated.smooth <- smooth_estimates(object = gam.model, data = pred)
  207. estimated.smooth <- estimated.smooth %>% select(smooth_var, est)
  208. return(estimated.smooth)
  209. }

GAMs_fixed.R at commit ed94e54, no license · at the source

Overview

Authors: De-Zhi Jin1, Changsong Zhou2, Xi-Nian Zuo3,4,5, Joshua Faskowitz6, Ting Xu7,8, Ye He1
  1. School of Artificial Intelligence, Beijing University of Posts and Telecommunications,Beijing, China
  2. Department of Physics, Centre for Nonlinear Studies and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University,Kowloon Tong, Hong Kong
  3. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University,Beijing, China
  4. National Basic Science Data Center, Beijing, China
  5. Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University,Beijing, China
  6. Department of Psychological and Brain Sciences, Indiana University,Bloomington, IN USA
  7. Center for the Integrative Developmental Neuroscience, Child Mind Institute,New York, NY USA
  8. Kunming Institute of Zoology, Chinese Academy of Sciences,Kunming, China
Journal: Nature communications, volume 17, issue 1, article 9138
Dates: received 19 September 2025; accepted 14 July 2026; published online 28 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-76011-7 · PMID 42649187 · PMCID PMC13518953 · OpenAlex W7171492208
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), systems (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Preprocessing, Connectivity, fMRI & imaging, Physiology & signal measures
Keywords: Cognitive neuroscience, Dynamic networks
MeSH: Nerve Net*, Sensorimotor Cortex*, Adolescent, Adult, Brain, Brain Mapping, Child, Female, Humans, Magnetic Resonance Imaging, Male, Young Adult (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Citations: cited by 1 paper (Europe PMC); 115 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.

Repositories

Its files are read in the Code ↔ Paper reader above, with 17 matches between paragraphs and lines of code.

zuoxinian/CCS

License: GPL-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 9a1fc10bb560f5a2aa802c7f6fcc80c5a44366ee, 12 September 2024
Languages: MATLAB (563), Python (90), Shell (74), Jupyter (2), R (1)
Size: 1,947 files, 730 scripts
Software Heritage: not archived
Found in: the text, “MRI data preprocessing”
Holds: README, license file, environment (H3/AmygdalaGo-BOLT/requirements_autodl.txt), 1 notebook
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: FreeSurfer (88 files), EEGLAB (75 files), PyTorch (55 files), FSL (42 files), NumPy (40 files), AFNI (21 files), Statistics and Machine Learning Toolbox (19 files), NiBabel (12 files), OpenCV (10 files), SimpleITK (10 files), GIfTI library for MATLAB (9 files), FieldTrip (8 files), ANTs (6 files), Image Processing Toolbox (5 files), Matplotlib (5 files), SciPy (5 files), SPM (4 files), Pillow (3 files), Brain Connectivity Toolbox (2 files), Signal Processing Toolbox (2 files), MONAI (2 files), Connectome Workbench (2 files), scikit-image (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
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dzjin5678/co-fluctuation-scores

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Commit: ed94e54c614fc0f2597236f626e81b7881080363, 5 June 2026
Languages: MATLAB (24), R (24)
Size: 88 files, 48 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (23 files), tidyverse (22 files), ggseg (21 files), Statistics and Machine Learning Toolbox (17 files), FieldTrip (6 files), Signal Processing Toolbox (4 files), BrainSpace (3 files), mgcv (3 files), ComplexHeatmap (1 file), SPM (1 file)
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Zenodo 20722002

License: CC-BY-4.0
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Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (23 files), tidyverse (22 files), ggseg (21 files), Statistics and Machine Learning Toolbox (17 files), FieldTrip (6 files), Signal Processing Toolbox (4 files), BrainSpace (3 files), mgcv (3 files), ComplexHeatmap (1 file), SPM (1 file)
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At the source:

Code availability statement

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Read it in the paper: doi.org/10.1038/s41467-026-76011-7.

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Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 2 keywords, 12 MeSH terms, 1 funder, 114 references.

Cite

This paper

Jin, D.-Z., Zhou, C., Zuo, X.-N., Faskowitz, J., Xu, T., & He, Y. (2026). Human cortex organizes dynamic co-fluctuations along the sensorimotor-association axis. Nature communications, 17(1), 9138. https://doi.org/10.1038/s41467-026-76011-7

BibTeX

@article{jin2026human,
author = {Jin, De-Zhi and Zhou, Changsong and Zuo, Xi-Nian and Faskowitz, Joshua and Xu, Ting and He, Ye},
title = {{Human cortex organizes dynamic co-fluctuations along the sensorimotor-association axis}},
journal = {Nature communications},
year = {2026},
month = jul,
volume = {17},
number = {1},
pages = {9138},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-76011-7},
url = {https://doi.org/10.1038/s41467-026-76011-7},
pmid = {42649187},
pmcid = {PMC13518953}
}

RIS

TY - JOUR
AU - Jin, De-Zhi
AU - Zhou, Changsong
AU - Zuo, Xi-Nian
AU - Faskowitz, Joshua
AU - Xu, Ting
AU - He, Ye
TI - Human cortex organizes dynamic co-fluctuations along the sensorimotor-association axis
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/07/28
VL - 17
IS - 1
SP - 9138
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-76011-7
UR - https://doi.org/10.1038/s41467-026-76011-7
LA - en
ER -

CSL-JSON

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"PMID": "42649187",
"PMCID": "PMC13518953",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-76011-7",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
28
]
]
}
}

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