Five-year associations among dopamine D2-like receptor loss, cognitive decline, education, and self-reported leisure activities in healthy older adults.
The 7 matches
- [1] § Method › Cognitive assessment ↔ Code/DataPreparation.R, lines 263–334 · score 0.92 · position recall, word recall, letter updating, letter comparison, perceptual speed, episodic memory
- [2] § Method › Statistical analyses ↔ Code/config.R, lines 47–134 · score 0.87 · right hemispheres, social activity frequency, exogenous variables, cognitive activity frequency, physical activity frequency, activity variables
- [3] § Method › Cognitive assessment ↔ Code/config.R, lines 47–134 · score 0.81 · position recall, word recall, letter updating, letter comparison, numerical, scores
- [4] § Method › Statistical analyses ↔ Code/DataPreparation.R, lines 44–132 · score 0.75 · sum scores, perceptual speed, episodic memory, working memory, ROI, putamen
- [5] § Method › Education and leisure activities ↔ Code/DataPreparation.R, lines 44–132 · score 0.74 · strength training, sum score, sociodemographic, jogging, walking, engagement
- [6] § Method › Data preparation ↔ Code/DataPreparation.R, lines 207–261 · score 0.62 · co registration, outliers, preparation, errors, segmentation, SD
- [7] § Method › Statistical analyses ↔ Code/config.R, lines 1–21 · score 0.57 · post burn, chains, iterations, variables
Paper
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The authors' code
R · 334 lines · 13 KB · no license · 4 matches
- # ============================================================================
- # Data Preparation for Bayesian SEM Analysis
- # COBRA Study 1 — Dopamine D2 Receptors, Cognition, Education, and Leisure
- # Author: Amos Pagin
- #
- # Note: This script requires the raw COBRA data files, which are not publicly
- # available due to Swedish data-protection regulations. Data access can be
- # requested from the authors for well-defined analysis projects consistent
- # with the original ethical approval (see manuscript for details).
- #
- # File paths below reference the project's internal data directory structure
- # and are provided for documentation purposes.
- # ============================================================================
- # Setup -------------------------------------------------------------------
- library(tidyverse)
- library(haven)
- library(readxl)
- # Helper: set intensity to NA when corresponding frequency is 0
- # This ensures intensity means only reflect activities actually performed.
- filter_intensity_by_freq <- function(df, freq_cols, int_cols) {
- stopifnot(length(freq_cols) == length(int_cols))
- for (i in seq_along(freq_cols)) {
- fc <- freq_cols[i]
- ic <- int_cols[i]
- if (fc %in% names(df) && ic %in% names(df)) {
- mask <- !is.na(df[[fc]]) & !is.na(df[[ic]]) & df[[fc]] == 0
- df[[ic]][mask] <- NA
- }
- }
- df
- }
- # Helper: standardize T2 using T1 mean and SD
- scale_t2_by_t1 <- function(t2_values, t1_values) {
- t1_mean <- mean(t1_values, na.rm = TRUE)
- t1_sd <- sd(t1_values, na.rm = TRUE)
- (t2_values - t1_mean) / t1_sd
- }
- # =========================================================================
- # 1. PET DATA
- # =========================================================================
- # PET BP_ND estimates (PVE-corrected, bilateral caudate/putamen/hippocampus)
- pet_wide <- read_csv("<path_to>/PET_bp_wide.csv")
- # T1
- pet_t1 <- pet_wide %>%
- select(id, contains(c("hippocampus", "caudate", "putamen"))) %>%
- select(-contains("ROI"), -contains("t2"))
- pet_t1$id <- gsub("C", "", pet_t1$id)
- pet_t1 <- pet_t1[, c(1, 2, 3, 6, 7, 10, 11)]
- colnames(pet_t1) <- c("id", "hc_left", "hc_right", "cau_left", "cau_right",
- "put_left", "put_right")
- # T2
- pet_t2 <- pet_wide %>%
- select(id, contains(c("hippocampus", "caudate", "putamen"))) %>%
- select(-contains("ROI"), -contains("t1"))
- pet_t2$id <- gsub("C", "", pet_t2$id)
- pet_t2 <- pet_t2[, c(1, 2, 3, 6, 7, 10, 11)]
- colnames(pet_t2) <- c("id", "hc_left_t2", "hc_right_t2", "cau_left_t2",
- "cau_right_t2", "put_left_t2", "put_right_t2")
- # Anatomical data (T1 only, for ROI definition)
- anat <- read_csv("<path_to>/anatomical_subcortical.csv") %>%
- filter(TimePoint == "t1") %>%
- select(SubjectId,
- `aseg:Left-Putamen(Volume_mm3)`, `aseg:Right-Putamen(Volume_mm3)`,
- `aseg:Left-Caudate(Volume_mm3)`, `aseg:Right-Caudate(Volume_mm3)`)
- colnames(anat) <- c("id", "put_left_anat", "put_right_anat",
- "cau_left_anat", "cau_right_anat")
- anat$id <- gsub("C", "", anat$id)
- # =========================================================================
- # 2. COGNITIVE DATA
- # =========================================================================
- # Task sum scores for working memory, episodic memory, and perceptual speed
- wmsum <- read_csv("<path_to>/WM-sumscores-T1-T2.csv")
- emsum <- read_csv("<path_to>/EM-sumscores-T1-T2.csv")
- pssum <- read_csv("<path_to>/PS-sumscores-T1-T2.csv")
- # =========================================================================
- # 3. BACKGROUND DATA
- # =========================================================================
- # Sociodemographic variables (age, sex, education, BMI)
- background_data <- read_sav("<path_to>/background_data.sav")
- background_data$id <- str_sub(background_data$id, start = 3)
- background_data <- background_data %>%
- rename(bmi = BMI1) %>%
- select(id, age1, male, yearsofeducation, bmi)
- # =========================================================================
- # 4. ACTIVITY DATA — T1 and T2
- # =========================================================================
- #
- # Column mapping in the COBRA questionnaire:
- # Cognitive frequency: F_12 to F_29 (18 items)
- # Cognitive intensity: F_30 to F_47 (18 items; F_N+18 maps to F_N)
- # Physical frequency: F_48 to F_62 (15 items)
- # Physical intensity: F_63 to F_77 (15 items; F_N+15 maps to F_N)
- # Social frequency: F_78 to F_87 (10 items; no intensity)
- #
- # All activities are included (no engagement cutoff).
- # Define column names
- cog_freq_cols <- paste0("F_", 12:29)
- cog_int_cols <- paste0("F_", 30:47)
- phys_freq_cols <- paste0("F_", 48:62)
- phys_int_cols <- paste0("F_", 63:77)
- soc_freq_cols <- paste0("F_", 78:87)
- # 5-activity physical intensity subset (Kohncke et al., 2018):
- # Walking (F_51), Cycling (F_52), Jogging (F_53), Strength training (F_55), Sports (F_61)
- # Corresponding intensity items: F_66, F_67, F_68, F_70, F_76
- intensity_5act_freq_cols <- c("F_51", "F_52", "F_53", "F_55", "F_61")
- intensity_5act_int_cols <- c("F_66", "F_67", "F_68", "F_70", "F_76")
- all_activity_cols <- c(cog_freq_cols, cog_int_cols,
- phys_freq_cols, phys_int_cols,
- soc_freq_cols)
- # --- Import and clean raw questionnaire data ---
- clean_activity_data <- function(filepath) {
- df <- read_excel(filepath)
- df <- rename(df, id = `C-nr`)
- df$id <- str_sub(df$id, start = 3)
- # Keep only id and activity columns (some columns may not exist in file)
- available_cols <- intersect(all_activity_cols, colnames(df))
- df <- df %>% select(id, all_of(available_cols))
- # Clean values
- df <- df %>%
- mutate(across(-id, ~ gsub("15\\+", "15", .))) %>%
- mutate(across(-id, ~ gsub("999", NA_character_, .))) %>%
- mutate(across(-id, ~ gsub("vet ej", NA_character_, .))) %>% # Swedish: "don't know"
- mutate(across(-id, ~ as.numeric(.)))
- df
- }
- act_t1 <- clean_activity_data("<path_to>/activity_questionnaire_wave1.xlsx")
- act_t2 <- clean_activity_data("<path_to>/activity_questionnaire_wave2.xlsx")
- # --- Apply intensity filtering: set intensity to NA if frequency = 0 ---
- act_t1 <- filter_intensity_by_freq(act_t1, phys_freq_cols, phys_int_cols)
- act_t1 <- filter_intensity_by_freq(act_t1, cog_freq_cols, cog_int_cols)
- act_t1 <- filter_intensity_by_freq(act_t1, intensity_5act_freq_cols, intensity_5act_int_cols)
- act_t2 <- filter_intensity_by_freq(act_t2, phys_freq_cols, phys_int_cols)
- act_t2 <- filter_intensity_by_freq(act_t2, cog_freq_cols, cog_int_cols)
- act_t2 <- filter_intensity_by_freq(act_t2, intensity_5act_freq_cols, intensity_5act_int_cols)
- # --- Compute T1 summary scores ---
- # Frequency sums (0 values contribute nothing, NA handled by na.rm)
- act_t1$phys_freq_sum <- rowSums(act_t1[phys_freq_cols], na.rm = TRUE)
- act_t1$cog_freq_sum <- rowSums(act_t1[cog_freq_cols], na.rm = TRUE)
- act_t1$soc_freq_sum <- rowSums(act_t1[soc_freq_cols], na.rm = TRUE)
- # Intensity means (only activities with freq > 0, thanks to filtering above)
- act_t1$phys_int_mean <- rowMeans(act_t1[phys_int_cols], na.rm = TRUE)
- act_t1$cog_int_mean <- rowMeans(act_t1[cog_int_cols], na.rm = TRUE)
- # 5-activity intensity mean (sensitivity analysis)
- act_t1$phys_int_5act_mean <- rowMeans(act_t1[intensity_5act_int_cols], na.rm = TRUE)
- # --- Compute T2 summary scores ---
- act_t2$phys_freq_sum <- rowSums(act_t2[phys_freq_cols], na.rm = TRUE)
- act_t2$cog_freq_sum <- rowSums(act_t2[cog_freq_cols], na.rm = TRUE)
- act_t2$soc_freq_sum <- rowSums(act_t2[soc_freq_cols], na.rm = TRUE)
- act_t2$phys_int_mean <- rowMeans(act_t2[phys_int_cols], na.rm = TRUE)
- act_t2$cog_int_mean <- rowMeans(act_t2[cog_int_cols], na.rm = TRUE)
- # 5-activity intensity mean (sensitivity analysis)
- act_t2$phys_int_5act_mean <- rowMeans(act_t2[intensity_5act_int_cols], na.rm = TRUE)
- # --- Reduce to summary columns ---
- act_t1_summary <- act_t1 %>%
- select(id, phys_freq_sum, cog_freq_sum, soc_freq_sum,
- phys_int_mean, cog_int_mean, phys_int_5act_mean) %>%
- rename_with(~ paste0(., "_t1"), -id)
- act_t2_summary <- act_t2 %>%
- select(id, phys_freq_sum, cog_freq_sum, soc_freq_sum,
- phys_int_mean, cog_int_mean, phys_int_5act_mean) %>%
- rename_with(~ paste0(., "_t2"), -id)
- act_summary <- full_join(act_t1_summary, act_t2_summary, by = "id")
- # =========================================================================
- # 5. MERGE ALL DATASETS
- # =========================================================================
- df <- full_join(pet_t1, pet_t2, by = "id")
- df <- full_join(df, anat, by = "id")
- df <- full_join(df, background_data, by = "id")
- df <- full_join(df, wmsum, by = "id")
- df <- full_join(df, emsum, by = "id")
- df <- full_join(df, pssum, by = "id")
- df <- full_join(df, act_summary, by = "id")
- # Composite bilateral PET measures
- df$bp_cau <- df$cau_left + df$cau_right
- df$bp_put <- df$put_left + df$put_right
- df$bp_hc <- df$hc_right + df$hc_left
- df$bp_cau_t2 <- df$cau_left_t2 + df$cau_right_t2
- df$bp_put_t2 <- df$put_left_t2 + df$put_right_t2
- df$bp_hc_t2 <- df$hc_right_t2 + df$hc_left_t2
- # =========================================================================
- # 6. EXCLUSIONS AND OUTLIER REMOVAL
- # =========================================================================
- # Remove subjects with known data issues (segmentation/co-registration errors)
- df <- df %>% filter(!id %in% c("036", "037", "113"))
- # Remove PET outliers (> 3 SD below mean for any ROI)
- df <- df %>%
- filter(scale(bp_cau) > -3) %>%
- filter(scale(bp_put) > -3) %>%
- filter(scale(bp_hc) > -3)
- # =========================================================================
- # 7. SCALE VARIABLES (T2 scaled using T1 mean and SD)
- # =========================================================================
- # --- DRD2 indicators (bilateral, by hemisphere) ---
- df$cau_left_z_t1 <- scale(df$cau_left)[,1]
- df$cau_left_z_t2 <- scale_t2_by_t1(df$cau_left_t2, df$cau_left)
- df$cau_right_z_t1 <- scale(df$cau_right)[,1]
- df$cau_right_z_t2 <- scale_t2_by_t1(df$cau_right_t2, df$cau_right)
- df$put_left_z_t1 <- scale(df$put_left)[,1]
- df$put_left_z_t2 <- scale_t2_by_t1(df$put_left_t2, df$put_left)
- df$put_right_z_t1 <- scale(df$put_right)[,1]
- df$put_right_z_t2 <- scale_t2_by_t1(df$put_right_t2, df$put_right)
- df$hc_left_z_t1 <- scale(df$hc_left)[,1]
- df$hc_left_z_t2 <- scale_t2_by_t1(df$hc_left_t2, df$hc_left)
- df$hc_right_z_t1 <- scale(df$hc_right)[,1]
- df$hc_right_z_t2 <- scale_t2_by_t1(df$hc_right_t2, df$hc_right)
- # --- Working Memory indicators ---
- # ll = letter updating, su = spatial updating, nb = numerical 3-back
- df$llsc1 <- scale(df$llsum1)[,1]
- df$llsc2 <- scale_t2_by_t1(df$llsum2, df$llsum1)
- df$susc1 <- scale(df$susum1)[,1]
- df$susc2 <- scale_t2_by_t1(df$susum2, df$susum1)
- df$nbsc1 <- scale(df$nbsum1)[,1]
- df$nbsc2 <- scale_t2_by_t1(df$nbsum2, df$nbsum1)
- # --- Episodic Memory indicators ---
- # rc = word recall, nrc = number-word recall, orc = object-position recall
- df$rcsc1 <- scale(df$rcsum)[,1]
- df$rcsc2 <- scale_t2_by_t1(df$rcsum2, df$rcsum)
- df$nrcsc1 <- scale(df$nrcsum)[,1]
- df$nrcsc2 <- scale_t2_by_t1(df$nrcsum2, df$nrcsum)
- df$orcsc1 <- scale(df$orcsum)[,1]
- df$orcsc2 <- scale_t2_by_t1(df$orcsum2, df$orcsum)
- # --- Perceptual Speed indicators ---
- # num = number comparison, fig = figure comparison, ver = letter comparison
- df$numsc1 <- scale(df$numsum)[,1]
- df$numsc2 <- scale_t2_by_t1(df$numsum2, df$numsum)
- df$figsc1 <- scale(df$figsum)[,1]
- df$figsc2 <- scale_t2_by_t1(df$figsum2, df$figsum)
- df$versc1 <- scale(df$versum)[,1]
- df$versc2 <- scale_t2_by_t1(df$versum2, df$versum)
- # --- Education ---
- df$education_sc <- scale(df$yearsofeducation)[,1]
- # --- Covariates for supplemental analyses ---
- # male is already 0/1; scale for consistency with other variables in the models
- df$male <- scale(df$male)[,1]
- df$bmi <- scale(df$bmi)[,1]
- # --- Activity measures (T1 scaled, T2 scaled by T1) ---
- df$physfreq_sc <- scale(df$phys_freq_sum_t1)[,1]
- df$physint_sc <- scale(df$phys_int_mean_t1)[,1]
- df$cogfreq_sc <- scale(df$cog_freq_sum_t1)[,1]
- df$cogint_sc <- scale(df$cog_int_mean_t1)[,1]
- df$socsum_sc <- scale(df$soc_freq_sum_t1)[,1]
- # 5-activity physical intensity (sensitivity analysis)
- df$physint_k5_sc <- scale(df$phys_int_5act_mean_t1)[,1]
- df$physfreq_t2_sc <- scale_t2_by_t1(df$phys_freq_sum_t2, df$phys_freq_sum_t1)
- df$physint_t2_sc <- scale_t2_by_t1(df$phys_int_mean_t2, df$phys_int_mean_t1)
- df$cogfreq_t2_sc <- scale_t2_by_t1(df$cog_freq_sum_t2, df$cog_freq_sum_t1)
- df$cogint_t2_sc <- scale_t2_by_t1(df$cog_int_mean_t2, df$cog_int_mean_t1)
- df$socsum_t2_sc <- scale_t2_by_t1(df$soc_freq_sum_t2, df$soc_freq_sum_t1)
- # 5-activity T2
- df$physint_k5_t2_sc <- scale_t2_by_t1(df$phys_int_5act_mean_t2, df$phys_int_5act_mean_t1)
- # =========================================================================
- # 8. MEDIAN SPLITS FOR MODERATION ANALYSES
- # =========================================================================
- df$education_group <- ifelse(df$education_sc > median(df$education_sc, na.rm = TRUE), "High", "Low")
- df$physfreq_group <- ifelse(df$physfreq_sc > median(df$physfreq_sc, na.rm = TRUE), "High", "Low")
- df$physint_group <- ifelse(df$physint_sc > median(df$physint_sc, na.rm = TRUE), "High", "Low")
- df$physint_k5_group <- ifelse(df$physint_k5_sc > median(df$physint_k5_sc, na.rm = TRUE), "High", "Low")
- df$cogfreq_group <- ifelse(df$cogfreq_sc > median(df$cogfreq_sc, na.rm = TRUE), "High", "Low")
- df$cogint_group <- ifelse(df$cogint_sc > median(df$cogint_sc, na.rm = TRUE), "High", "Low")
- df$socsum_group <- ifelse(df$socsum_sc > median(df$socsum_sc, na.rm = TRUE), "High", "Low")
DataPreparation.R, no license · at the source
Overview
- Department of Psychology, University of Gothenburg, Gothenburg, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
- Department of Diagnostics and Intervention, Umeå University, Umeå, Sweden
- Aging Research Center, Karolinska Institute and Stockholm University, Solna, Sweden
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
- Max Planck Centre for Computational Psychiatry and Ageing Research, London, United Kingdom
Abstract
Age-related loss of dopamine (DA) integrity has been linked to cognitive decline. Relatedly, education and leisure activity engagement have been highlighted as neurocognitive protective factors, but their associations with DA integrity remain poorly understood. Using Bayesian structural equation modeling, we analyzed longitudinal data from the Cognition, Brain, and Aging (COBRA) prospective cohort study with 181 older adults at baseline to examine correlations among DA D2-like receptor (DRD2) availability in the caudate and putamen, measured using [11C]raclopride positron emission tomography (PET), cognition (working memory, episodic memory, and perceptual speed), education, and self-reported physical, cognitive, and social leisure activity measures. Our research questions target whether (i) education or leisure activities are associated with baseline levels or 5-year changes in DRD2 availability; (ii) changes in leisure activities covary with DRD2 changes; and (iii) education or leisure activities moderate DRD2–cognition change–change correlations. Results showed declines in DRD2 availability in the caudate and putamen, with weak overall DRD2–cognition change–change correlations. For both baseline levels and changes in DRD2 availability, the associations with education and leisure activities were uniformly negligible or small and not strongly supported. Neither education nor leisure activities moderated DRD2–cognition change–change correlations.
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 7 matches between paragraphs and lines of code.
OSF pwy8f
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
3 files
- Code/
DataPreparation.R , R, 334 lines, 4 matches - Code/
config.R , R, 134 lines, 3 matches - Code/
model_syntax.R , R, 304 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;
- 3 scripts, each with its path and the digest of its content;
- 7 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 and Code Availability
Swedish data-protection laws prohibit us from providing the data in the public domain, but data can be requested from the authors and subsequently transferred for well-defined analysis projects that are in line with the one covered by the original ethical approval. Complete model outputs and code used for the analyses are provided at the OSF repository: 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 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 8 authors, 6 keywords, 6 funders, 90 references.
Cite
This paper
Pagin, A., Karalija, N., Andersson, M., Nyberg, L., Bäckman, L., Riklund, K., Lindenberger, U., & Lövdén, M. (2026). Five-year associations among dopamine D2-like receptor loss, cognitive decline, education, and self-reported leisure activities in healthy older adults. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1302. https://
BibTeX
@article{pagin2026five,
author = {Pagin, Amos and Karalija, Nina and Andersson, Micael and Nyberg, Lars and Bäckman, Lars and Riklund, Katrine and Lindenberger, Ulman and Lövdén, Martin},
title = {{Five-year associations among dopamine D2-like receptor loss, cognitive decline, education, and self-reported leisure activities in healthy older adults}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = jul,
volume = {4},
pages = {IMAG.a.1302},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/
url = {https://
pmid = {42488356},
pmcid = {PMC13389743}
}
RIS
TY - JOUR
AU - Pagin, Amos
AU - Karalija, Nina
AU - Andersson, Micael
AU - Nyberg, Lars
AU - Bäckman, Lars
AU - Riklund, Katrine
AU - Lindenberger, Ulman
AU - Lövdén, Martin
TI - Five-year associations among dopamine D2-like receptor loss, cognitive decline, education, and self-reported leisure activities in healthy older adults
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/
VL - 4
SP - IMAG.a.1302
SN - 2837-6056
PB - MIT Press
DO - 10.1162/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "Imaging neuroscience (Cambridge, Mass.)",
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"family": "Pagin",
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"page": "IMAG.a.1302",
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}
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