Long-term memory reorganization of navigational episodes.
The 5 matches
- [1] § Methods › Statistical analysis ↔ Analysis/OSF_BZT_retro_correlation_regression_models_171125.R, lines 264–330 · score 0.69 · 6–10000, pairwise contrasts, pairwise comparisons, cross, slopes, regression
- [2] § Methods › Statistical analysis ↔ Analysis/OSF_BZT_retro_ebbinghaus_simulation_171125.R, lines 130–204 · score 0.61 · Post hoc, SS, marginal, residual, sum, prediction
- [3] § Results › Memory of real-world navigational episodes also depends on time-independent factors ↔ Analysis/OSF_BZT_retro_generalized_additive_model_161125.R, lines 46–115 · score 0.60 · generalized additive model, zoo visitors, education, GAM, age, target placement
- [4] § Methods › Statistical analysis ↔ Analysis/OSF_BZT_retro_ebbinghaus_simulation_171125.R, lines 130–204 · score 0.55 · post hoc, simulated, marginal, Ebbinghaus, minutes, pairwise
- [5] § Results › Memory of real-world navigational episodes transforms nonlinearly across decades ↔ Analysis/OSF_BZT_retro_correlation_regression_models_171125.R, lines 264–330 · score 0.51 · regression models, Pairwise comparisons, slopes, fitting, power, zoo visit
Paper
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The authors' code
R · 444 lines · 17 KB · no license · 2 matches
- # ------------------------------------------------------------------------------
- # :::::::::::: libraries :::::::::::::::::::::::::::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # data
- library(readxl)
- library(officer)
- library(tidyverse)
- # statistic
- library(effectsize)
- library(emmeans)
- library(rstatix)
- library(diffcor)
- # Model
- library(afex)
- library(splines)
- library(mgcv)
- # ------------------------------------------------------------------------------
- # :::::::::::::::::::::::: Read in Data ::::::::::::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # questionnaire
- qn_zVisit <- read_excel("C:/.../OSF_BZT_retro_zooVisit_data.xlsx", col_names = TRUE)
- # Target placement data
- data_distance <- read_excel("C:/.../OSF_BZT_retro_targetPlacement_accuracyScore_data.xlsx", col_names = TRUE)
- # Direction-Pointing data (without North)
- data_deviation <- read_excel("C:/..../OSF_BZT_retro_directionPointing_data.xlsx", col_names = TRUE)
- # ------------------------------------------------------------------------------
- # ::::::::::::::::::::: Data preparation :::::::::::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # aggregate experimental data per id and group
- data_dist <- data_distance %>% group_by(id,zooVisit) %>% summarise(
- zscore_dist = mean(z_as*-1,na.rm = TRUE), .groups = "drop")
- data_dist$id <- as.double(data_dist$id)
- data_dev <- data_deviation %>% group_by(id, zooVisit) %>% summarise(
- zscore_dev_b = mean(deviation_zscore_pointing_arrow, na.rm = TRUE),
- zscore_dev_ub = mean(deviation_zscore_pointing_video, na.rm = TRUE),
- .groups = "drop")
- # Merge datasets
- data_merged <- reduce(list(qn_zVisit, data_dev, data_dist), full_join, by = c("id", "zooVisit"))
- # select data
- data_visitor <- subset(data_merged, data_merged$zooVisit==1) # subset zoo-visitor
- # ------------------------------------------------------------------------------
- # :::::::::::::::::::: Pairwise Correlation & correlation matrix :::::::::::::::
- # ------------------------------------------------------------------------------
- # pairwise correlations
- # direction-pointing with arrow vs. direction-pointing with video
- cor_devb_devub <- cor.test(data_visitor$zscore_dev_b,data_visitor$zscore_dev_ub,
- method=c( "spearman"))
- # target placement vs. direction-pointing with video
- cor_dist_devub <- cor.test(data_visitor$zscore_dev_ub,data_visitor$zscore_dist,
- method=c( "spearman"))
- # target placement vs. direction-pointing with arrow
- cor_dist_devb <- cor.test(data_visitor$zscore_dev_b,data_visitor$zscore_dist,
- method=c( "spearman"))
- # Get correlation matrix
- # select data
- cor_zooVisit <- data_visitor %>%
- dplyr::select(zscore_dev_ub,zscore_dev_b,zscore_dist,time_last_zooVisit_days)
- corr.mat <- cor_mat(round(cor_zooVisit), method = "spearman",
- alternative = "two.sided", conf.level = 0.95)
- corrp.mat <- cor_pmat(round(cor_zooVisit), method = "spearman", conf.level = 0.95)
- print(corr.mat)
- print(corrp.mat)
- # Comparison of correlations
- n_obs = 104
- # last visit
- diffcor.dep(corr.mat$time_last_zooVisit_days[1], corr.mat$time_last_zooVisit_days[2],
- cor_devb_devub[["estimate"]][["rho"]], n_obs, cor.names = NULL,
- alternative = c( "two.sided"), digit = 3)
- diffcor.dep(corr.mat$time_last_zooVisit_days[1], corr.mat$time_last_zooVisit_days[3],
- cor_dist_devub[["estimate"]][["rho"]], n_obs, cor.names = NULL,
- alternative = c( "two.sided"), digit = 3)
- diffcor.dep(corr.mat$time_last_zooVisit_days[3], corr.mat$time_last_zooVisit_days[2],
- cor_dist_devb[["estimate"]][["rho"]], n_obs, cor.names = NULL,
- alternative = c( "two.sided"), digit = 3)
- # ------------------------------------------------------------------------------
- # :::::::::::::::::::::: Model memory consolidation ::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # ------------------------------------------------------------------------------
- # Prepare data for models
- # ------------------------------------------------------------------------------
- prepare_model_data <- function(df, zscore_var, knots_vec) {
- df %>%
- dplyr::select(id, zscore = {{zscore_var}}, time_last_zooVisit_days) %>%
- na.omit() %>%
- list(knots = knots_vec)
- }
- data_list <- list(
- devub = prepare_model_data(data_visitor, zscore_dev_ub, c(180, 2000, 4000, 7500)),
- devb = prepare_model_data(data_visitor, zscore_dev_b, c(180, 1000, 2000, 6500)),
- dist = prepare_model_data(data_visitor, zscore_dist, c(180, 1000, 4000, 6000))
- )
- # ------------------------------------------------------------------------------
- # LOOCV Function
- # ------------------------------------------------------------------------------
- run_loocv_models <- function(data, knots) {
- models <- list(
- linear = function(train) lm(zscore ~ time_last_zooVisit_days, data = train),
- log = function(train) lm(zscore ~ log(time_last_zooVisit_days), data = train),
- exp = function(train) lm(log(zscore + 2) ~ time_last_zooVisit_days, data = train),
- power = function(train) lm(log(zscore + 2) ~ log(time_last_zooVisit_days), data = train),
- quadratic = function(train) lm(zscore ~ poly(time_last_zooVisit_days, 2, raw = TRUE), data = train),
- cubic = function(train) lm(zscore ~ poly(time_last_zooVisit_days, 3, raw = TRUE), data = train),
- spline = function(train) lm(zscore ~ bs(time_last_zooVisit_days, knots = knots), data = train),
- gam = function(train) gam(zscore ~ s(time_last_zooVisit_days), data = train)
- )
- evaluate_model <- function(model_name, model_fun) {
- fit_full <- tryCatch(model_fun(data), error = function(e) NULL)
- loocv_errors <- sapply(1:nrow(data), function(i) {
- test <- data[i, ]
- train <- data[-i, ]
- fit <- tryCatch(model_fun(train), error = function(e) NULL)
- if (is.null(fit)) return(NA)
- pred <- tryCatch(predict(fit, newdata = test), error = function(e) NA)
- if (is.na(pred)) return(NA)
- pred_adj <- if (model_name %in% c("exp", "power")) exp(pred) - 2 else pred
- (pred_adj - test$zscore)^2
- })
- mse <- mean(loocv_errors, na.rm = TRUE)
- rmse <- sqrt(mse)
- residuals <- tryCatch({
- full_pred <- predict(fit_full)
- full_pred_adj <- if (model_name %in% c("exp", "power")) exp(full_pred) - 2 else full_pred
- full_pred_adj - data$zscore
- }, error = function(e) rep(NA, nrow(data)))
- rse <- sqrt(mean(residuals^2, na.rm = TRUE))
- mod_summary <- tryCatch(summary(fit_full), error = function(e) NULL)
- r2 <- if (!is.null(mod_summary)) mod_summary$r.squared else NA
- r2_adj <- if (!is.null(mod_summary)) mod_summary$adj.r.squared else NA
- fstat <- if (!is.null(mod_summary) && !is.null(mod_summary$fstatistic)) mod_summary$fstatistic else NA
- fval <- if (!is.null(fstat)) unname(fstat["value"]) else NA
- df1 <- if (!is.null(fstat)) fstat["numdf"] else NA
- df2 <- if (!is.null(fstat)) fstat["dendf"] else NA
- pval <- if (!is.na(fval) && !is.na(df1) && !is.na(df2)) pf(fval, df1, df2, lower.tail = FALSE) else NA
- data.frame(
- model = model_name,
- AIC = round(tryCatch(AIC(fit_full), error = function(e) NA), 4),
- BIC = round(tryCatch(BIC(fit_full), error = function(e) NA), 4),
- RSE = round(rse, 4),
- MSE = round(mse, 4),
- RMSE = round(rmse, 4),
- R2 = if (!is.null(r2) && is.numeric(r2)) round(r2, 4) else NA,
- R2_adj = if (!is.null(r2_adj) && is.numeric(r2_adj)) round(r2_adj, 4) else NA,
- F_value = round(fval, 4),
- p_value = signif(pval, 4)
- )
- }
- results <- do.call(rbind, Map(evaluate_model, names(models), models))
- return(results)
- }
- # ------------------------------------------------------------------------------
- # run datasets
- # ------------------------------------------------------------------------------
- results_dist <- run_loocv_models(data_list$dist[[1]], data_list$dist$knots)
- results_dev_b <- run_loocv_models(data_list$devb[[1]], data_list$devb$knots)
- results_dev_ub <- run_loocv_models(data_list$devub[[1]], data_list$devub$knots)
- # ------------------------------------------------------------------------------
- # Results
- # ------------------------------------------------------------------------------
- # Combined results
- all_results <- rbind(results_dist, results_dev_b, results_dev_ub)
- print(all_results)
- # ------------------------------------------------------------------------------
- # ::::::::::: Get best model according to AIC ::::::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # Best model AIC
- best_aic_dist <- results_dist[which.min(results_dist$AIC), ]
- best_aic_dev_b <- results_dev_b[which.min(results_dev_b$AIC), ]
- best_aic_dev_ub <- results_dev_ub[which.min(results_dev_ub$AIC), ]
- print(best_aic_dist)
- print(best_aic_dev_b)
- print(best_aic_dev_ub)
- # ------------------------------------------------------------------------------
- # Addition: generalize additive model (for R2 and test statistic)
- # ------------------------------------------------------------------------------
- gam_devub.fit <- gam((data_visitor$zscore_dev_ub) ~ s(data_visitor$time_last_zooVisit_days))
- summary(gam_devub.fit)
- print(gam_devub.fit)
- gam_devb.fit <- gam((data_visitor$zscore_dev_b) ~ s(data_visitor$time_last_zooVisit_days))
- summary(gam_devb.fit)
- print(gam_devb.fit)
- gam_dist.fit <- gam((data_visitor$zscore_dist) ~ s(data_visitor$time_last_zooVisit_days))
- summary(gam_dist.fit)
- print(gam_dist.fit)
- # ------------------------------------------------------------------------------
- # :::::::::::::::: Task comparison per model :::::::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # Reshape data for comparison
- data_visitor_response <- pivot_longer(data_visitor,
- cols = c('zscore_dist', 'zscore_dev_ub', 'zscore_dev_b'),
- names_to = 'task',
- values_to = 'response')
- # Prepare the data for modeling
- data_visitor_allTasks <- data_visitor_response %>% dplyr::select( id, response,
- task, time_last_zooVisit_days)
- data_visitor_allTasks <- na.omit(data_visitor_allTasks)
- # ------------------------------------------------------------------------------
- # Fit models
- # ------------------------------------------------------------------------------
- # Power-transformed model
- power_all.fit <- lm(log(response + 2) ~ task * log(time_last_zooVisit_days), data = data_visitor_allTasks)
- anova_power <- anova(power_all.fit)
- omega_squared(power_all.fit, partial = FALSE)
- anova_power
- # ------------------------------------------------------------------------------
- # Trends per task
- # ------------------------------------------------------------------------------
- decay_rates <- emtrends( power_all.fit,specs = ~ task,var = "log(time_last_zooVisit_days)")
- decay_sum <- summary(decay_rates)
- decay_sum <- decay_sum %>%
- mutate(
- estimate = `log(time_last_zooVisit_days).trend`,
- t_value = estimate / SE,
- p_value = 2 * pt(abs(t_value), df, lower.tail = FALSE),
- r_effect = sqrt((t_value^2) / (t_value^2 + df))
- )
- decay_sum
- # ------------------------------------------------------------------------------
- # Comparison of slopes
- # ------------------------------------------------------------------------------
- # compare pairs of regression curves
- emtrends_power <- pairs(emtrends(power_all.fit,specs=pairwise~task,var="time_last_zooVisit_days"))
- # Pairwise comparison of slopes
- pairs_slopes <- pairs(emtrends_power)
- print(pairs_slopes)
- # ------------------------------------------------------------------------------
- # ::::::::::::: pairwise contrasts between tasks :::::::::::::::::::::::::::::::
- # ------------------------------------------------------------------------------
- # Define time grid (every 10 days from 6 to 10,000)
- time_points <- seq(6, 10000, by = 10)
- # Define levels
- tasks <- levels(data_visitor_allTasks$task)
- # Data with timepoint and task
- newdata <- expand.grid(
- time_last_zooVisit_days = time_points,
- task = tasks
- )
- newdata$log_time <- log(newdata$time_last_zooVisit_days)
- # Emmeans per combination
- emm_list <- emmeans(
- object = power_all.fit,
- specs = ~ task | time_last_zooVisit_days,
- at = list(time_last_zooVisit_days = time_points)
- )
- # Pairwise contrasts per timepoint
- contrast_results <- summary(pairs(emm_list), infer = TRUE)
- # Prepare dataframe and extract timepoints
- all_results <- as.data.frame(contrast_results) %>%
- mutate(
- time_last_zooVisit_days = as.numeric(as.character(time_last_zooVisit_days))
- )
- # Filter for significant contrasts
- significant_results <- all_results %>%
- filter(p.value < 0.05)
- # For each contrast, identify the earliest day from which it remains significant
- significant_summary <- significant_results %>%
- group_by(contrast) %>%
- summarise(
- first_signif_day = min(time_last_zooVisit_days),
- last_signif_day = max(time_last_zooVisit_days)
- )
- print(significant_summary)
- # Output
- print(significant_results[, c("time_last_zooVisit_days", "contrast", "estimate", "p.value")])
- # ------------------------------------------------------------------------------
- # Crossing mean of control group (zoo-naive)
- # ------------------------------------------------------------------------------
- # Mean & SD (Attention: lower value => upper SD)
- calculate_mean_and_upper_sd <- function(data, zscore_col, group_var) {
- mean_val <- mean(data[[zscore_col]][data[[group_var]] == 2], na.rm = TRUE)
- sd_val <- sd(data[[zscore_col]][data[[group_var]] == 2], na.rm = TRUE)
- upper_sd_val <- mean_val - sd_val # Attention
- return(list(mean = mean_val, upper_sd = upper_sd_val))
- }
- # z-scores
- zscore_vars <- c("zscore_dev_ub", "zscore_dev_b", "zscore_dist")
- result_list <- list()
- # run function
- for (zscore_var in zscore_vars) {
- result_list[[zscore_var]] <- calculate_mean_and_upper_sd(data_merged, zscore_var, "zooVisit")
- }
- # ------------------------------------------------------------------------------
- # Power-Regressions per z-score
- # ------------------------------------------------------------------------------
- calculate_time_values <- function(data, zscore_col, mean_value, upper_sd_value) {
- # Power Regression
- power_fit <- lm(log(get(zscore_col) + 2) ~ log(time_last_zooVisit_days), data = data)
- # Coefficients
- beta_0 <- coef(power_fit)[1]
- beta_1 <- coef(power_fit)[2]
- # How many days to reach mean of control group
- time_for_mean <- exp((log(mean_value + 2) - beta_0) / beta_1)
- # How many days to reach SD of control group
- time_for_upper_sd <- exp((log(upper_sd_value + 2) - beta_0) / beta_1)
- # years
- time_for_mean_years <- time_for_mean / 365
- time_for_upper_sd_years <- time_for_upper_sd / 365
- # Return list of results
- return(list(
- beta_0 = beta_0,
- beta_1 = beta_1,
- time_for_mean_days = time_for_mean,
- time_for_upper_sd_days = time_for_upper_sd,
- time_for_mean_years = time_for_mean_years,
- time_for_upper_sd_years = time_for_upper_sd_years
- ))
- }
- # calculation per z-score
- time_values_list <- list()
- # run datasets
- for (zscore_var in zscore_vars) {
- time_values_list[[zscore_var]] <- calculate_time_values(data_visitor, zscore_var,
- result_list[[zscore_var]]$mean,
- result_list[[zscore_var]]$upper_sd)
- }
- # Results
- time_values_list
- # ------------------------------------------------------------------------------
- # Get values for three decades per equation/ z-score
- # ------------------------------------------------------------------------------
- # get list of timepoints
- timepoint_list <- list(time_last_zooVisit_days = seq(0.1, 365 * 30, by = 365 / 4))
- # get list of variables
- zscore_columns <- c("zscore_dev_ub", "zscore_dev_b", "zscore_dist")
- # table of results
- result_table <- data.frame(
- time_last_zooVisit_days = timepoint_list$time_last_zooVisit_days,
- zscore_dev_ub = NA,
- zscore_dev_b = NA,
- zscore_dist = NA
- )
- # get results per z-score
- for (i in 1:length(zscore_columns)) {
- zscore_col <- zscore_columns[i]
- # Fit model
- power.fit <- lm(log(get(zscore_col) + 2) ~ log(time_last_zooVisit_days), data = data_visitor)
- # calculate estimated means
- emmeans_result <- emmeans(power.fit, ~ time_last_zooVisit_days, at = timepoint_list)
- # get mean and upper and lower CL
- summary_result <- summary(emmeans_result)
- # table
- result_table[[zscore_col]] <- paste(
- round(summary_result$emmean, 3),
- "(",
- round(summary_result$lower.CL, 3),
- "-",
- round(summary_result$upper.CL, 3),
- ")"
- )
- }
- # prepare word document
- doc <- read_docx()
- doc <- doc %>%
- body_add_table(value = result_table, style = "table_template")
- print(doc, target = "OSF_BZT_retro_zscore_results_30years.docx")
OSF_BZT_retro_correlation_regression_models_171125.R, no license · at the source
Overview
- Department of Neurology, Charité-Universitätsmedizin Berlin,Berlin, Germany
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin,Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin,Berlin, Germany
- Berlin University of Applied Sciences,Berlin, Germany
Abstract
During navigation, the brain builds representations of self-motion and of environmental information for future action. The classic view suggests that these representations consolidate and eventually stabilize. However, there are no data on their fate at extended memory delays. Here we investigated memory of real-world navigational episodes across memory delays of up to three decades. We show that memory of the spatial aspects of these episodes do not achieve a stable state but rather continue to transform for many years. Our data suggest that at any given point in time, spatial memory of navigational episodes is a changing combination of episode-independent schematic information and several interacting spatial representations directly related to a navigational episode, which may show distinct temporal trajectories. Consistent with recent accounts of memory reorganization, we further show that neither current theories of systems consolidation nor classic models of forgetting fully explain spatial memory performance at extended memory delays.
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 5 matches between paragraphs and lines of code.
OSF sb65k
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
- 28 September 2026: the link answers (HTTP 200)
8 files
- Analysis/
OSF_BZT_randomization_pe , MATLAB, 406 linesrmutation_bootstrapping. m - Analysis/
OSF_BZT_retro_correlatio , R, 444 lines, 2 matchesn_regression_models_1711 25.R - Analysis/
OSF_BZT_retro_correlatio , R, 97 linesns_selfLocalization_task s_161125.R - Analysis/
OSF_BZT_retro_descriptiv , R, 213 linese_comparison_visitor_non visitor_161125.R - Analysis/
OSF_BZT_retro_ebbinghaus , R, 204 lines, 2 matches_simulation_171125.R - Analysis/
OSF_BZT_retro_generalize , R, 115 lines, 1 matchd_additive_model_161125. R - Analysis/
OSF_BZT_retro_randomizat , MATLAB, 361 linesiontest_comparison_16112 5.m - Analysis/
OSF_BZT_retro_recent_rem , R, 343 linesote_1_10_30_230326.R
Code availability
The R and MATLAB code of this study are available via OSF at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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;
- 8 scripts, each with its path and the digest of its content;
- 5 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
The data and R code of this study are available via OSF 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 → Nature Portfolio
Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 4 MeSH terms, 3 funders, 42 references.
Cite
This paper
Iggena, D., Schmelter, T., Maier, P. M., Reguieg, K., Finke, C., Hildebrand, K., & Ploner, C. J. (2026). Long-term memory reorganization of navigational episodes. Nature human behaviour, 10(7), 1327-1339. https://
BibTeX
@article{iggena2026long,
author = {Iggena, Deetje and Schmelter, Thereza and Maier, Patrizia M. and Reguieg, Khaled and Finke, Carsten and Hildebrand, Kristian and Ploner, Christoph J.},
title = {{Long-term memory reorganization of navigational episodes}},
journal = {Nature human behaviour},
year = {2026},
month = may,
volume = {10},
number = {7},
pages = {1327--1339},
publisher = {Nature Portfolio},
issn = {2397-3374},
doi = {10.1038/
url = {https://
pmid = {42151554},
pmcid = {PMC13388105}
}
RIS
TY - JOUR
AU - Iggena, Deetje
AU - Schmelter, Thereza
AU - Maier, Patrizia M.
AU - Reguieg, Khaled
AU - Finke, Carsten
AU - Hildebrand, Kristian
AU - Ploner, Christoph J.
TI - Long-term memory reorganization of navigational episodes
T2 - Nature human behaviour
J2 - Nat Hum Behav
PY - 2026
DA - 2026/
VL - 10
IS - 7
SP - 1327
EP - 1339
SN - 2397-3374
PB - Nature Portfolio
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"title": "Long-term memory reorganization of navigational episodes",
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"given": "Deetje"
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