What makes a lonely child: environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study.
The 11 matches
- [1] § Methods › Health › Physical health ↔ scripts/03_health.R, lines 190–279 · score 0.93 · sleep wake transition, excessive somnolence, sleep breathing, maintaining sleep, arousal, vision
- [2] § Results › Multimodal neural correlates of prospective loneliness ↔ scripts/06_rsfc.R, lines 156–212 · score 0.87 · fronto parietal, cingulo parietal, cingulo opercular, left pallidum, right caudate, mouth
- [3] § Results › Familial and broader environmental correlates of prospective loneliness ↔ scripts/02_exposome.R, lines 262–321 · score 0.82 · witnessing domestic violence, planned pregnancy, family conflict, family income, twin, Parental
- [4] § Methods › Health › Mental health ↔ scripts/03_health.R, lines 190–279 · score 0.81 · rule breaking, mental health, Prodromal, aggressive, anxious, somatic
- [5] § Methods › Environment ↔ scripts/02_exposome.R, lines 322–381 · score 0.76 · Neighborhood Socioeconomic Status, Neighborhood Safety, School Environment, Pollution, Family
- [6] § Methods › Brain MRI data acquisition and preprocessing ↔ scripts/14_gmv_sens_incident.R, lines 64–131 · score 0.76 · imgincl t1w, mrif_score, family ID, intracranial, winsorized, GMV
- [7] § Methods › Brain MRI data acquisition and preprocessing ↔ scripts/04_gmv.R, lines 66–140 · score 0.75 · imgincl t1w, mrif_score, family ID, intracranial, winsorized, GMV
- [8] § Results › Multimodal neural correlates of prospective loneliness ↔ scripts/06_rsfc.R, lines 156–212 · score 0.61 · cingulo opercular, left pallidum, right caudate, salience
- [9] § Methods › Associations of environment and health with prospective loneliness ↔ scripts/06_rsfc.R, lines 265–346 · score 0.59 · logistic regression, binomial, logit, mixed, models, ethnicity
- [10] § Methods › Associations of environment and health with prospective loneliness ↔ scripts/04_gmv.R, lines 191–272 · score 0.58 · logistic regression, binomial, logit, mixed, models, ethnicity
- [11] § Methods › Health › Mental health ↔ scripts/02_exposome.R, lines 382–443 · score 0.58 · mental health, anxious, somatic, thought, externalizing, depressed
Paper
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The authors' code
R · 346 lines · 10 KB · MIT · 3 matches
- # Environment ------------------------------------------------------------------
- library(tidyverse)
- library(lme4)
- library(ggseg)
- library(patchwork)
- library(here)
- library(glue)
- library(ggraph)
- library(igraph)
- source(here("src", "R", "plot_ggseg_brain.R"))
- source(here("src", "R", "run_lda_workflow.R"))
- # Data I/O ---------------------------------------------------------------------
- master_preprocessed_df <- here(
- "data", "processed", "master_preprocessed_df.rds"
- ) %>%
- read_rds()
- # using data release 5.1
- # please change the path to ABCD study folder
- abcd_folder_path <- "/Users/tywong/OneDrive/opendata/abcd" %>%
- here("abcd-data-release-5.1/core")
- # general
- mri_y_qc_clfind <- here(abcd_folder_path, "imaging", "mri_y_qc_clfind.csv") %>%
- read_csv(show_col_types = FALSE)
- mri_y_qc_incl <- here(abcd_folder_path, "imaging", "mri_y_qc_incl.csv") %>%
- read_csv(show_col_types = FALSE)
- mri_y_adm_info <- here(abcd_folder_path, "imaging", "mri_y_adm_info.csv") %>%
- read_csv(show_col_types = FALSE) %>%
- select(src_subject_id, eventname, mri_info_deviceserialnumber)
- mri_y_qc_motion <- here(abcd_folder_path, "imaging", "mri_y_qc_motion.csv") %>%
- read_csv(show_col_types = FALSE)
- # RSFC variables
- rsfc_variables_df <- here("data", "raw", "included_variables.xlsx") %>%
- readxl::read_excel(sheet = "RSFC")
- selected_filenames <- c(unique(pull(rsfc_variables_df, table_name)))
- selected_variables <- c(pull(rsfc_variables_df, variable_name)) # 416
- selected_files <- list()
- for (ith in seq_along(selected_filenames)) {
- selected_files[[ith]] <- list.files(
- path = abcd_folder_path,
- full.names = TRUE,
- pattern = glue("{selected_filenames[ith]}.csv"),
- recursive = TRUE
- ) %>%
- read_csv(show_col_types = FALSE) %>%
- select(src_subject_id, eventname, any_of(selected_variables))
- }
- master_rsfc_df <- selected_files %>%
- reduce(left_join, by = c("src_subject_id", "eventname")) %>%
- left_join(mri_y_qc_clfind, by = c("src_subject_id", "eventname")) %>%
- left_join(mri_y_qc_incl, by = c("src_subject_id", "eventname")) %>%
- left_join(mri_y_adm_info, by = c("src_subject_id", "eventname")) %>%
- left_join(mri_y_qc_motion, by = c("src_subject_id", "eventname")) %>%
- filter(eventname == "baseline_year_1_arm_1") %>%
- mutate(
- across(where(is.numeric), ~na_if(., 777)),
- across(where(is.numeric), ~na_if(., 999))
- ) %>%
- filter(
- # https://docs.abcdstudy.org/latest/documentation/imaging/type_qc.html
- mrif_score %in% c(1, 2) & imgincl_t1w_include == 1,
- imgincl_rsfmri_include == 1
- ) %>%
- select(src_subject_id:rsfmri_cor_ngd_vta_scs_vtdcrh, rsfmri_meanmotion,
- mri_info_deviceserialnumber) %>%
- right_join(master_preprocessed_df, by = "src_subject_id") %>%
- drop_na() # only complete data
- find_identical_columns <- function(df) {
- col_names <- colnames(df)
- n <- length(col_names)
- identical_pairs <- list()
- for (i in 1:(n - 1)) {
- for (j in (i + 1):n) {
- if (identical(df[[i]], df[[j]])) {
- identical_pairs[[length(identical_pairs) + 1]] <-
- c(col1 = col_names[i], col2 = col_names[j])
- }
- }
- }
- if (length(identical_pairs) == 0) {
- message("No identical columns found.")
- return(invisible(NULL))
- }
- do.call(rbind, identical_pairs) |> as.data.frame()
- }
- identical_labels <- master_rsfc_df %>%
- find_identical_columns() %>%
- pull(col2)
- rsfc_labels <- master_rsfc_df %>%
- select(rsfmri_c_ngd_ad_ngd_ad:rsfmri_cor_ngd_vta_scs_vtdcrh) %>%
- select(-all_of(identical_labels)) %>%
- colnames() # 33
- master_rsfc_resid_df <- master_rsfc_df
- for (ith in seq_along(rsfc_labels)) {
- cat(sprintf("\rExtract residuals: %d / %d", ith, length(rsfc_labels)))
- label <- rsfc_labels[ith]
- # perform Fisher's z transformation
- master_rsfc_resid_df[[label]] <- atanh(master_rsfc_resid_df[[label]])
- formula_ <- glue::glue(
- "{label} ~ loneliness_bl + interview_age + demo_sex_v2 + \
- race_ethnicity_3 + rsfmri_meanmotion + \
- (1 | mri_info_deviceserialnumber) + (1 | rel_family_id)"
- ) %>%
- as.formula()
- master_rsfc_resid_df[[label]] <- master_rsfc_df %>%
- mutate(
- !!label := as.numeric(scale(.data[[label]]))
- ) %>%
- lmer(
- formula = formula_,
- control = lmerControl(
- optimizer = "bobyqa", optCtrl = list(maxfun = 2e5)
- )
- ) %>%
- resid() %>%
- scale() %>%
- as.numeric()
- }
- rsfc_lda_result <- run_lda_workflow(
- df = master_rsfc_resid_df,
- target = "loneliness_fu_any",
- predictors = rsfc_labels,
- n_bootstraps = 1000,
- alpha = 0.05,
- replace = TRUE
- )
- rsfc_lda_result$bal_acc_mean
- rsfc_lda_result$bal_acc_sd
- rsfc_lda_result$roc_auc_mean
- rsfc_lda_result$roc_auc_sd
- rsfc_lda_result %>%
- left_join(rsfc_variables_df, by = "variable_name") %>%
- select(variable_name, from, to, mean_weight, ci_low, ci_high, is_sig) %>%
- mutate_if(is.numeric, round, digits = 3) %>%
- rename(
- "LDA weight" = "mean_weight",
- "95% CI (Lower)" = "ci_low",
- "95% CI (Upper)" = "ci_high",
- "Significant?" = "is_sig"
- ) %>%
- write_csv(here("outputs", "tables", "lda_results_rsfc.csv"))
- rsfc_lda_sig_result <- rsfc_lda_result %>%
- left_join(rsfc_variables_df, by = "variable_name") %>%
- select(variable_name, from, to, mean_weight, ci_low, ci_high, is_sig) %>%
- filter(is_sig) %>%
- select(from, to, mean_weight) %>%
- mutate(from = case_when(
- from == "cingulo-parietal" ~ "CPT",
- from == "fronto-parietal" ~ "FPN",
- from == "salience" ~ "SAL",
- from == "sensorimotor mouth" ~ "SML",
- from == "cingulo-opercular" ~ "COP"
- )) %>%
- mutate(to = case_when(
- to == "visual" ~ "VIS",
- to == "none" ~ "NON",
- to == "salience" ~ "SAL",
- to == "left-pallidum" ~ "L Pallidum",
- to == "right-caudate" ~ "R Caudate"
- )) %>%
- mutate(col = ifelse(mean_weight > 0, "#CE204E", "#395D9C"))
- library(circlize)
- node_colors <- c(
- CPT = "#006dfe",
- NON = "#c1c0be",
- FPN = "#f3e601",
- SAL = "#0a0a08",
- SML = "#ff7f00",
- VIS = "#3a469a",
- COP = "#810080",
- `L Pallidum` = "#666666",
- `R Caudate` = "#666666"
- )
- circos.clear()
- pdf(here("outputs", "figures", "chord_diagram_plot.pdf"), width = 5, height = 5)
- chordDiagram(
- x = rsfc_res,
- grid.col = node_colors,
- col = rsfc_res$col,
- transparency = 0.3,
- annotationTrack = "grid",
- preAllocateTracks = 1
- )
- # Add inner labels
- circos.trackPlotRegion(
- track.index = 1,
- panel.fun = function(x, y) {
- circos.text(
- x = CELL_META$xcenter,
- y = CELL_META$ylim[1] - 0.25,
- labels = CELL_META$sector.index,
- facing = "bending.inside",
- col = "white",
- niceFacing = TRUE,
- adj = c(0.5, 0.5),
- cex = 0.8
- )
- },
- bg.border = NA,
- track.height = 0.1
- )
- dev.off()
- highlight_df <- tibble::tibble(
- label = c("Left-Pallidum", "Right-Caudate"),
- highlight = TRUE
- )
- # Join with aseg and plot
- aseg_highlighted_vis <- highlight_df %>%
- brain_join(aseg) %>%
- reposition_brain(position = "coronal") %>%
- ggplot() +
- geom_sf(
- aes(fill = highlight),
- color = "black"
- ) +
- scale_fill_manual(
- values = c("TRUE" = "#666666", "FALSE" = "gray85"),
- na.value = "gray85"
- ) +
- theme_void() +
- theme(legend.position = "none")
- ggsave(
- plot = aseg_highlighted_vis,
- filename = here("outputs", "figures", "aseg_highlighted.pdf"),
- device = cairo_pdf,
- width = 4,
- height = 4
- )
- # Logistic Regression ----------------------------------------------------------
- rsfc_lr_res_list <- list()
- for (ith in 1:(length(rsfc_labels))) {
- cat(sprintf("\rRSFC Running: %d / %d", ith, length(rsfc_labels)))
- rsfc_var <- rsfc_labels[ith]
- f1 <- glue::glue(
- "loneliness_fu_any ~ {rsfc_var} + loneliness_bl + demo_sex_v2 + \
- interview_age + race_ethnicity_3 + (1 | site_id_l) + \
- (1 | rel_family_id)"
- ) |>
- as.formula()
- res <- master_rsfc_df |>
- mutate(!!rsfc_var := as.numeric(scale(.data[[rsfc_var]]))) |>
- glmer(
- formula = f1,
- family = binomial(link = "logit"),
- control = glmerControl(tolPwrss = 1e-10)
- ) |>
- parameters::model_parameters(
- effect = "fixed",
- verbose = FALSE
- ) |>
- as_tibble() |>
- dplyr::slice(2) |>
- mutate(
- cohend = effectsize::logoddsratio_to_d(Coefficient, log = TRUE),
- cohend_low = effectsize::logoddsratio_to_d(CI_low, log = TRUE),
- cohend_high = effectsize::logoddsratio_to_d(CI_high, log = TRUE),
- variable_name = rsfc_var,
- .before = "p"
- )
- rsfc_lr_res_list[[ith]] <- res
- }
- rsfc_res_df <- tibble(
- variable_name = rsfc_lda_result$weights$variable_name,
- lr_weights = rsfc_lr_res_list |> reduce(bind_rows) |> pull(cohend),
- lda_weights = rsfc_lda_result$weights$mean_weight
- )
- cor_results <- correlation::correlation(rsfc_res_df)
- r_val <- cor_results$r[1]
- p_val <- cor_results$p[1]
- label_text <- sprintf("italic(r) == %.2f*','~~italic(p) == %.2g", r_val, p_val)
- rsfc_comp_fig <- rsfc_res_df |>
- ggplot(aes(x = lda_weights, y = lr_weights)) +
- geom_point(size = 4, color = "gray30", alpha = 0.75, shape = 16) +
- geom_smooth(method = "lm", color = "tomato3", fill = "tomato2") +
- annotate(
- "text",
- x = -Inf, y = Inf,
- label = label_text,
- parse = TRUE,
- hjust = -0.1, vjust = 1.5,
- size = 4.5
- ) +
- labs(
- title = "Resting-state Functional Connectivity",
- x = "Mean LDA Weights (Bootstrapped, n = 1,000)",
- y = "Cohen's d from Mixed-effects Logistic Regression"
- ) +
- ggthemes::theme_pander() +
- theme(
- plot.margin = margin(5, 5, 5, 5, "mm"),
- plot.title.position = "plot"
- )
- rsfc_comp_fig
- ggsave(
- plot = rsfc_comp_fig,
- filename = here("outputs", "figures", "rsfc_comp_fig.pdf"),
- width = 6,
- height = 5
- )
06_rsfc.R at commit bc774c6, under MIT · at the source
Overview
14 affiliations
- Department of Psychology, The Education University of Hong Kong, Hong Kong Special Administrative Region, China
- Centre for Psychosocial Health, The Education University of Hong Kong, Hong Kong Special Administrative Region, China
- AI, Brain and Child Research Centre (ABC‐RC), Academy of Educational Development and Innovation, The Education University of Hong Kong, Hong Kong Special Administrative Region, China
- SWU‐EdUHK Joint Lab for Research on Brain, Education, and Intelligence (BEI Lab), Hong Kong Special Administrative Region, China
- Independent Data Analyst, Nagoya City, Japan
- Analytics\Assessment Research Centre, The Education University of Hong Kong, Hong Kong Special Administrative Region, China
- Focus Program Translational Neuroscience, Neuroimaging Center, Johannes Gutenberg University Medical Center, Mainz, Germany
- Leibniz Institute for Resilience Research, Mainz, Germany
- Department of Psychiatry, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Psychiatry, Brain Behavior Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute (LiBI), Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
Abstract
Background: Loneliness in childhood is a growing public health concern, yet early multilevel candidate risk and protective factors remain insufficiently mapped. Systematic investigation is essential to guide prevention and intervention during sensitive developmental periods. This study identifies environmental, health, and neurobiological factors associated with prospective loneliness in children.
Methods: A population‐based longitudinal cohort study used data from children aged 9–10 years and their caregivers enrolled in the Adolescent Brain Cognitive Development (ABCD) Study between 2016 and 2022. A total of 9,602 children with complete baseline and follow‐up loneliness and demographic data were included after exclusions for exposure completeness and quality assurance. Baseline measures included 347 environmental exposures, 61 health indicators, and 558 MRI features capturing gray matter volume, white matter microstructure, and resting‐state functional connectivity. The primary outcome was prospective loneliness reported from ages 10–14. Linear mixed‐effects models assessed associations with environmental and health variables. Linear discriminant analysis was applied to neuroimaging features to distinguish children with and without prospective loneliness.
Results: Among 9,602 children (mean [SD] age, 119.01 [7.52] months; 48% girls; 55% White, 14% Black, 31% other races/
Conclusions: Prospective loneliness was associated with modifiable environmental and health factors, as well as neurobiological differences. Early identification and targeted interventions that support socioemotional development, particularly within family, neighborhood, and school contexts, may help mitigate loneliness and its long‐term impact.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.
lonilab/abcd_prospective_loneliness
bc774c6b877603767f4d888222c3a02db2942c1e, 8 April 2026Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
28 files
- scripts/
01_preprocessing.R , R, 333 lines - scripts/
02_exposome.R , R, 443 lines, 3 matches - scripts/
03_health.R , R, 280 lines, 2 matches - scripts/
04_gmv.R , R, 272 lines, 2 matches - scripts/
05_wmt.R , R, 263 lines - scripts/
06_rsfc.R , R, 346 lines, 3 matches - scripts/
07_exposome_sens_firstye , R, 271 linesar.R - scripts/
08_health_sens_firstyear , R, 234 lines.R - scripts/
09_gmv_sens_firstyear.R , R, 190 lines - scripts/
10_wmt_sens_firstyear.R , R, 185 lines - scripts/
11_rsfc_sens_firstyear.R , R, 207 lines - scripts/
12_exposome_sens_inciden , R, 274 linest.R - scripts/
13_health_sens_incident. , R, 235 linesR - scripts/
14_gmv_sens_incident.R , R, 191 lines, 1 match - scripts/
15_wmt_sens_incident.R , R, 181 lines - scripts/
16_rsfc_sens_incident.R , R, 210 lines - scripts/
17_exposome_sens_prepand , R, 274 linesemic.R - scripts/
18_health_sens_prepandem , R, 235 linesic.R - scripts/
19_gmv_sens_prepandemic. , R, 193 linesR - scripts/
20_wmt_sens_prepandemic. , R, 187 linesR - scripts/
21_rsfc_sens_prepandemic , R, 211 lines.R - src/
R/ , R, 135 linesCopyOfrun_lda_workflow_o rg.R - src/
R/ , R, 5 linesis_binary_column.R - src/
R/ , R, 69 linesplot_ggseg_brain.R - src/
R/ , R, 63 linesrun_lda_performance.R - src/
R/ , R, 137 linesrun_lda_workflow.R - LICENSE, License, 27 lines
- README.md, Text, 82 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 26 scripts, each with its path and the digest of its content;
- 11 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability statement
The data that support the findings of this study are openly available in the NIMH Data Archive (NDA) at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Data Availability Statement
The data utilized in this study were sourced from the ABCD Study (https://
The data that support the findings of this study are openly available in the NIMH Data Archive (NDA) at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 2, 28 September 2026
- Publisher: n/a → Wiley
Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 4 keywords, 10 MeSH terms, 2 funders, 87 references.
Cite
This paper
Wong, T. Y., Wong, T. S., Hou, W. K., Leung, A. N. M., Xiao, J., Yuen, K. S. L., Lui, S. S. Y., Qiu, A., Moore, T. M., & Gur, R. C. (2026). What makes a lonely child: environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study. Journal of child psychology and psychiatry, and allied disciplines, 67(10), 1714-1728. https://
BibTeX
@article{wong2026what,
author = {Wong, Ting Yat and Wong, Ting Sam and Hou, Wai Kai and Leung, Angel Nga Man and Xiao, Jie and Yuen, Kenneth S L and Lui, Simon S Y and Qiu, Anqi and Moore, Tyler M and Gur, Ruben C},
title = {{What makes a lonely child: environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study}},
journal = {Journal of child psychology and psychiatry, and allied disciplines},
year = {2026},
month = may,
volume = {67},
number = {10},
pages = {1714--1728},
publisher = {Wiley},
issn = {0021-9630},
doi = {10.1111/
url = {https://
pmid = {42186177},
pmcid = {PMC13535708}
}
RIS
TY - JOUR
AU - Wong, Ting Yat
AU - Wong, Ting Sam
AU - Hou, Wai Kai
AU - Leung, Angel Nga Man
AU - Xiao, Jie
AU - Yuen, Kenneth S L
AU - Lui, Simon S Y
AU - Qiu, Anqi
AU - Moore, Tyler M
AU - Gur, Ruben C
TI - What makes a lonely child: environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study
T2 - Journal of child psychology and psychiatry, and allied disciplines
J2 - J Child Psychol Psychiatry
PY - 2026
DA - 2026/
VL - 67
IS - 10
SP - 1714
EP - 1728
SN - 0021-9630
PB - Wiley
DO - 10.1111/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1111/
"type": "article-journal",
"title": "What makes a lonely child: environmental, health, and multimodal neuroimaging correlates of prospective loneliness in the ABCD study",
"container-title": "Journal of child psychology and psychiatry, and allied disciplines",
"author": [
{
"family": "Wong",
"given": "Ting Yat"
},
{
"family": "Wong",
"given": "Ting Sam"
},
{
"family": "Hou",
"given": "Wai Kai"
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{
"family": "Leung",
"given": "Angel Nga Man"
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{
"family": "Xiao",
"given": "Jie"
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{
"family": "Yuen",
"given": "Kenneth S L"
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{
"family": "Lui",
"given": "Simon S Y"
},
{
"family": "Qiu",
"given": "Anqi"
},
{
"family": "Moore",
"given": "Tyler M"
},
{
"family": "Gur",
"given": "Ruben C"
}
],
"container-title-short":
"volume": "67",
"issue": "10",
"page": "1714-1728",
"DOI": "10.1111/
"PMID": "42186177",
"PMCID": "PMC13535708",
"ISSN": "0021-9630",
"publisher": "Wiley",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
25
]
]
}
}
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