OSCR

Light Exposure as a Modifiable Determinant of Mental Health.

Code ↔ Paper

3 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 3 matches
  1. [1] § Using Light Exposure to Study Mental Health: Measurement and Intervention Opportunities › Observational Characterization of Light Exposure in Mental Health Conditions ↔ scripts/desc_analysis.qmd, lines 270–413 · score 0.77 · melanopic EDI, Low daytime, low nighttime, High daytime, consecutive, S010
  2. [2] § Using Light Exposure to Study Mental Health: Measurement and Intervention Opportunities › Observational Characterization of Light Exposure in Mental Health Conditions ↔ scripts/Figure_3.qmd, lines 131–168 · score 0.76 · melanopic EDI, Low daytime, low nighttime, High daytime, consecutive, S010
  3. [3] § Monitoring Compliance and Dose in Light Therapy Studies ↔ scripts/Figure_4.qmd, lines 114–149 · score 0.68 · post light, melanopic EDI, pre light, therapy light, Figure 4

Paper

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The authors' code

Quarto · 414 lines · 12 KB · CC-BY-4.0 · 1 match

  1. ---
  2. title: "Descriptive analysis"
  3. author: "Johannes Zauner"
  4. format:
  5. html:
  6. self-contained: true
  7. code-tools: true
  8. ---
  9. # Preface
  10. This is a work-in-progress descriptive analysis of the `Sancho-SalasEtAl2025` dataset.
  11. ```{r}
  12. #| label: setup
  13. #| include: false
  14. library(LightLogR)
  15. library(glue)
  16. library(tidyverse)
  17. library(gt)
  18. library(readxl)
  19. library(cowplot)
  20. library(legendry)
  21. library(rnaturalearth)
  22. library(rnaturalearthdata)
  23. library(sf)
  24. library(patchwork)
  25. library(rlang)
  26. library(here)
  27. source("https://raw.githubusercontent.com/MeLiDosProject/Data_Metadata_Conventions/main/scripts/overview_plot.R")
  28. source(
  29. "https://raw.githubusercontent.com/MeLiDosProject/Data_Metadata_Conventions/main/scripts/summary_table.R"
  30. )
  31. ```
  32. # Overview
  33. ## Data import: wearable data
  34. The first step is the import of wearable data from the `head` position (mounted on glasses).
  35. ```{r}
  36. #| label: "general information"
  37. #time zone of Costa Rica
  38. tz <- "America/Costa_Rica"
  39. #coordinates for Costa Rica
  40. coordinates <- c(9.9372, -84.0509)
  41. #regex to extract participant Id and wearing position
  42. # pattern <- "[A-Z]+_S[0-9]{3}_[hcw]"
  43. #regex to extract participant Id
  44. # pattern <- "^([0-9]{3})_"
  45. pattern <- "(UCRS[0-9]{3})_"
  46. country_colors <- c(
  47. Sweden = "#88CCEE", # Sky blue
  48. Spain = "#CC6677", # Coral red
  49. Germany = "#DDCC77", # Mustard yellow
  50. Netherlands= "#117733", # Dark green
  51. Turkey = "#332288", # Indigo
  52. Ghana = "#AA4499", # Purple-pink
  53. Costa_Rica = "#44AA99" # Teal
  54. )
  55. ```
  56. ```{r}
  57. #path to participants
  58. path_part1 <- "data/raw/individual"
  59. #path to actlumus data sans wearing position
  60. path_part2 <- "/continuos/actlumus_"
  61. #wearing position
  62. wearing_position <- "chest"
  63. #getting all subfolders
  64. folders <- dir(here(path_part1))
  65. #creating complete folder names
  66. paths <- glue("{path_part1}/{folders}{path_part2}{wearing_position}")
  67. #collecting file names
  68. files <- list.files(here(paths), full.names = TRUE)
  69. files <- files[str_detect(files, "Report", negate = TRUE)]
  70. ```
  71. ```{r}
  72. #there remain some early data from a pilot collection. these will be removed
  73. data <- import$ActLumus(files, tz, auto.id = pattern, dst_adjustment = TRUE)
  74. #change names to conform to group
  75. data <-
  76. data |>
  77. mutate(Id = fct_relabel(Id, \(x) sprintf("UCR_S%03d", parse_number(x))))
  78. ```
  79. ```{r}
  80. paths_cc <- glue("{path_part1}/{folders}/continuos/currentconditions")
  81. #collecting file names
  82. files_cc <- list.files(here(paths_cc), full.names = TRUE)
  83. current_conditions <- read_csv(files_cc)
  84. current_conditions <-
  85. current_conditions |>
  86. select(Id = record_id, start = startdate_4_v2,
  87. currentlight = currentight_v2, kss = kss_v2) |>
  88. mutate(start = force_tz(start, tz),
  89. start = start - dminutes(30),
  90. end = start + dhours(1),
  91. Id = factor(Id)) |>
  92. drop_na(start) |>
  93. group_by(Id)
  94. ```
  95. ```{r}
  96. #| fig-width: 10
  97. #| fig-height: 5
  98. data <-
  99. data |>
  100. select(Id, Datetime, MEDI) |>
  101. add_states(current_conditions)
  102. data |>
  103. filter(Id %in% c("UCRS001", "UCRS002")) |>
  104. gg_days() |>
  105. gg_state(currentlight, aes_fill = currentlight)
  106. data |>
  107. filter(Id %in% c("UCRS001", "UCRS002", "UCRS003")) |>
  108. gg_heatmap() +
  109. geom_point(data = \(x) x |> drop_na(currentlight),
  110. aes(col = currentlight), size = 4) +
  111. scale_color_manual(values = c(E = "yellow2", I = "skyblue3", L = "green2", O = "skyblue", S = "green3"))
  112. ```
  113. ## Regularizing data
  114. In the first step, we will trim the data by the study time.
  115. ```{r}
  116. #import table with study times
  117. Study_dates <- read_excel("../data/Study_dates_MeLiDos_UCR.xlsx")
  118. #gather the important information
  119. Study_dates <-
  120. Study_dates |>
  121. rename(Id = subjectID_device, start = date_trial_start, end = date_trial_end) |>
  122. select(Id, start, end) |>
  123. mutate(across(c(start, end), \(x) force_tz(x, tz)),
  124. trial = TRUE) |>
  125. drop_na() |>
  126. filter(str_detect(Id, "_c$")) |>
  127. mutate(
  128. Id = str_remove(Id, "_c$"),
  129. Id = factor(Id)) |>
  130. group_by(Id)
  131. #add the trim information to the dataset and filter by it
  132. data <-
  133. data |>
  134. add_states(Study_dates) |>
  135. dplyr::filter(trial) |>
  136. select(-trial)
  137. data |> gg_overview()
  138. # data |> summarize(min = min(Datetime), max = max(Datetime))
  139. ```
  140. ```{r}
  141. data |> has_gaps()
  142. data |> has_irregulars()
  143. data |> gg_gaps(group.by.days = TRUE, show.irregulars = TRUE, full.days = FALSE)
  144. ```
  145. ```{r}
  146. #| fig-height: 15
  147. #| fig-width: 5
  148. data_cleaned <- data |> gap_handler(full.days = TRUE)
  149. data_cleaned |> gap_table(MEDI) |> cols_hide(ends_with("_n"))
  150. ```
  151. ## Exporting hourly values
  152. ```{r}
  153. data_export <-
  154. data_cleaned |>
  155. aggregate_Datetime("1 minute", numeric.handler = \(x) mean(x, na.rm = TRUE)) |>
  156. remove_partial_data(MEDI, threshold.missing = "3 hours", by.date = TRUE)
  157. save(data_export, file = "../data/imported/light/cr_1minute.RData")
  158. ```
  159. ## Visualization
  160. ```{r}
  161. #| warning: false
  162. #| message: false
  163. #| fig-height: 8
  164. #| fig-width: 12
  165. data_cleaned |>
  166. mutate(Id = fct_relabel(Id, \(x) str_remove(x, "UCR_"))) |>
  167. grand_overview(coordinates, "San José", "Costa Rica", "#44AA99", photoperiod_sequence = 0.2, ov_y.text.size = 5)
  168. ggsave("../output/figures/Figure_1.png", width = 17, height = 10, scale = 2, units = "cm")
  169. ggsave("../output/figures/Figure_1.pdf", width = 17, height = 10, scale = 2, units = "cm")
  170. ```
  171. ```{r}
  172. #| message: false
  173. #| warning: false
  174. table_summary <-
  175. light_summary_table(
  176. data_cleaned, coordinates, "San Pedro, San José", "Costa Rica", country_colors["Costa_Rica"],
  177. histograms = TRUE
  178. )
  179. table_summary
  180. gtsave(table_summary, here("output/tables/table_summary.png"), vwidth = 820)
  181. gtsave(table_summary, here("output/tables/table_summary.pdf"))
  182. gtsave(table_summary |> cols_hide(c(plot)), here("output/tables/table_summary.docx"))
  183. ```
  184. ## Adding sleep information
  185. ```{r}
  186. #path to participants
  187. path_part1 <- "data/raw/individual"
  188. #path to sleep diary
  189. path_part3 <- "/continuos/sleepdiary"
  190. #getting all subfolders
  191. folders <- dir(here(path_part1))
  192. #creating complete folder names
  193. paths <- glue("{path_part1}/{folders}{path_part3}")
  194. #collecting file names
  195. files <- list.files(here(paths), full.names = TRUE)
  196. sleep_data <-
  197. import_Statechanges(filename = files[c(3,9,10)],
  198. # sep = ";",
  199. # sep = ",",
  200. # dec = ",",
  201. Id.colname = record_id,
  202. Datetime.format = "mdYHM",
  203. tz = tz,
  204. State.colnames = c("sleep_v2", "offset_v2"),
  205. State.encoding = c("sleep", "wake")
  206. )
  207. #adjusting sleeptime for S009
  208. sleep_data[7,3] <- sleep_data[7,3] + dhours(3)
  209. Brown_data <-
  210. sleep_data |>
  211. sc2interval(full = TRUE, starting.state = "wake") |>
  212. LightLogR::sleep_int2Brown(
  213. Brown.day = "wake",
  214. Brown.evening = "pre-s",
  215. Brown.night = "sleep"
  216. ) |>
  217. mutate(Id = fct_relabel(Id, \(x) sprintf("UCR_S%03d", parse_number(x))))
  218. ```
  219. ## Single out extreme patterns
  220. ```{r}
  221. #| eval: false
  222. #| fig-width: 7
  223. #| fig-height: 7
  224. data_5min <-
  225. data_cleaned |>
  226. select(Id, Datetime, MEDI) |>
  227. aggregate_Datetime("5 mins", numeric.handler = \(x) mean(x, na.rm = TRUE)) |>
  228. remove_partial_data(
  229. MEDI, by.date = TRUE,
  230. ) |>
  231. mutate(.Date = (date(Datetime) - min(date(Datetime)) + 1))
  232. dose_data <-
  233. data_5min |>
  234. add_Date_col(group.by = TRUE) |>
  235. summarize(
  236. dose(
  237. MEDI,
  238. Datetime,
  239. na.rm = TRUE,
  240. as.df = TRUE
  241. ),
  242. .groups = "drop"
  243. )
  244. dose_data |>
  245. ungroup() |>
  246. filter(dose == max(dose) | dose == min(dose))
  247. data_5min |>
  248. gg_day(facetting = FALSE,
  249. group = factor(.Date),
  250. geom = "line",
  251. aes_col = factor(.Date)) +
  252. facet_wrap(~Id, ncol = 2)
  253. data_5min_red <-
  254. data_5min |>
  255. filter(Id %in% c("UCR_S010", "UCR_S003", "UCR_S009"))
  256. data_5min_red <-
  257. data_5min_red |>
  258. interval2state(Brown_data, State.colname = State.Brown) |>
  259. Brown2reference(
  260. Brown.day = "wake",
  261. Brown.evening = "pre-s",
  262. Brown.night = "sleep"
  263. ) |>
  264. mutate(State.Brown = fct_relevel(State.Brown,
  265. "wake", "pre-s", "sleep"))
  266. Plot1 <-
  267. data_5min_red |>
  268. # filter(Id %in% c("UCR_S010") & date(Datetime) == "2025-07-12") |> #High day low night
  269. # filter(Id %in% c("UCR_S003") & date(Datetime) == "2025-06-19") |> #High night
  270. # filter(Id %in% c("UCR_S009") & date(Datetime) == "2025-07-05") |> #low day
  271. filter(date(Datetime) %in% c("2025-07-12", "2025-07-05", "2025-06-19")) |>
  272. # filter(date(Datetime) %in% c("2025-07-01", "2025-07-05")) |>
  273. add_Date_col() |>
  274. add_photoperiod(coordinates) |>
  275. mutate(Id = fct_relevel(Id, "UCR_S010", "UCR_S003", "UCR_S009"),
  276. Id = fct_recode(Id,
  277. "High daytime & low nighttime levels" = "UCR_S010",
  278. "High nighttime levels" = "UCR_S003",
  279. "Low daytime levels" = "UCR_S009"),
  280. # Id = fct_reorder(Id, MEDI, .fun = min, .desc = TRUE),
  281. ) |>
  282. gg_doubleplot(alpha = 0.8,
  283. aes_col = State.Brown,
  284. group = consecutive_id(State.Brown),
  285. # aes_col = factor(Id),
  286. aes_fill = State.Brown,
  287. # aes_fill = factor(Id),
  288. facetting = FALSE,
  289. y.axis.label = "Melanopic EDI (lx)") |>
  290. gg_photoperiod() +
  291. guides(fill = "none", color = "none") +
  292. facet_wrap(~Id, scales = "free_x", ncol = 1) +
  293. coord_cartesian(ylim = c(0,20000)) +
  294. labs(x = NULL) +
  295. theme(
  296. strip.background = element_blank()
  297. ) +
  298. ggplot2::theme_sub_axis(text = element_text(size = 10)) +
  299. theme_sub_strip(text = element_text(face = "bold"))
  300. Plot2 <-
  301. data_5min_red |>
  302. filter(date(Datetime) %in% c("2025-07-12", "2025-07-05", "2025-06-19")) |>
  303. mutate(Id = fct_relevel(Id, "UCR_S010", "UCR_S003", "UCR_S009"),
  304. Id = fct_recode(Id,
  305. " " = "UCR_S010",
  306. " " = "UCR_S003",
  307. " " = "UCR_S009")) |>
  308. group_by(
  309. State.Brown, .add = TRUE
  310. ) |>
  311. summarize(
  312. mean = mean(MEDI, na.rm = TRUE), .groups = "drop"
  313. ) |>
  314. ggplot(aes(x = State.Brown, y = mean)) +
  315. geom_col(aes(fill = State.Brown)) +
  316. facet_wrap(~Id, ncol = 1, scales = "free_x") +
  317. scale_y_continuous(trans = "symlog",
  318. breaks = c(0, 10^(0:5)),
  319. labels =
  320. function(x) format(rep("", 7),
  321. scientific = FALSE, big.mark = " ")) +
  322. coord_cartesian(ylim = c(0,20000)) +
  323. cowplot::theme_cowplot() +
  324. ggsci::scale_fill_jco() +
  325. guides(fill = "none") +
  326. labs(y = "Melanopic EDI (lx)",
  327. x = NULL
  328. ) +
  329. # geom_text(aes(y = 0,
  330. # label = State.Brown |> str_replace("-sleep", "-slp")),
  331. # vjust = -0.1, size = 3) +
  332. # annotate(geom = "text",
  333. # x = 1, y = 20000, label = "wake", color = "black",
  334. # angle = 90, hjust = 1, size = 4)+
  335. # annotate(geom = "text",
  336. # x = 2, y = 20000, label = "pre-sleep", color = "black",
  337. # angle = 90, hjust = 1, size = 4)+
  338. # annotate(geom = "text",
  339. # x = 3, y = 20000, label = "sleep", color = "black",
  340. # angle = 90, hjust = 1, size = 4)+
  341. ggplot2::theme(plot.title.position = "plot",
  342. strip.text.y = ggplot2::element_text(face = "bold",
  343. ), strip.placement = "outside",
  344. panel.grid.major.y = ggplot2::element_line("grey95"),
  345. strip.background = element_blank(),
  346. # strip.text = element_blank(),
  347. plot.margin = ggplot2::margin(10,
  348. 20, 10, 10, "pt")) +
  349. ggplot2::theme_sub_axis(text = element_text(size = 10))
  350. Plot1 + plot_spacer() + Plot2 + plot_layout(widths = c(6,-0.4, 1), axes = "collect")
  351. ggsave("../output/figures/Figure_patterns.png", width = 8*1.5, height = 7*1.5, scale = 2, units = "cm")
  352. ```

desc_analysis.qmd at commit ed90d9a, under CC-BY-4.0 · at the source

Overview

  1. Department Health and Sports Sciences, TUM School of Medicine and Health, Chronobiology & Health, Technical University of Munich, Munich, Germany
  2. Max Planck Institute for Biological Cybernetics, Max Planck Research Group Translational Sensory & Circadian Neuroscience, Tübingen, Germany
  3. TUM Institute for Advanced Study (TUM-IAS), Technical University of Munich, Garching, Germany
  4. TUMCREATE Ltd., Singapore, Singapore
Journal: Current psychiatry reports, volume 28, issue 1, article 24
Dates: received 9 February 2026; accepted 9 March 2026; published online 28 April 2026; in print 2026
Type: Review · Language: English
License: CC BY
Identifiers: DOI 10.1007/s11920-026-01671-7 · PMID 42047992 · PMCID PMC13124800 · OpenAlex W7157141178
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), clinical / translational (subfield)
Keywords: Light Exposure, Mental Health, Circadian Rhythms, Exposome, Non-Visual Photoreception, Light-Based Interventions
MeSH: Circadian Rhythm*, Light*, Mental Disorders*, Mental Health*, Phototherapy*, Humans (* major topic)
Topic: Circadian rhythm and melatonin (Endocrine and Autonomic Systems, Neuroscience), according to OpenAlex
Funding: Wellcome Trust (226944); Max Planck Institute for Biological Cybernetics
Citations: not cited yet (Europe PMC); 78 references in the paper

Abstract

Purpose of Review: Light is a fundamental environmental signal that shapes human physiology, behaviour, and mental health. Beyond vision, light exposure regulates circadian rhythms, sleep, neuroendocrine function, arousal, and brain circuits implicated in emotional regulation. This review synthesizes recent evidence linking light exposure to mental health and argues that light should be conceptualized as a core, modifiable component of the mental health exposome – the cumulative, dynamic set of environmental influences shaping mental health across the lifespan.

Recent Findings: Recent randomized controlled trials using light therapy, large-scale epidemiological studies, and neurophysiological investigations demonstrate that habitual patterns of daytime and nighttime light exposure are associated with a broad range of mental health outcomes. Higher daytime light exposure is generally associated with better mood and lower depressive symptomatology, whereas greater exposure to light at night is linked to increased risk of depression, anxiety, and sleep disturbance. Advances in wearable light measurement and digital phenotyping now enable precise characterization of individual light environments, supporting observational studies and improving dose verification in light-based interventions. Emerging neurobiological evidence further suggests that light can influence affective brain circuits through pathways that extend beyond sleep and circadian regulation.

Summary: Together, converging evidence positions light exposure as a biologically potent and highly modifiable determinant of mental health operating across multiple temporal scales, from acute alerting effects to longer-term circadian and behavioural adaptation. Conceptual challenges remain, including bidirectionality between light exposure and mental health and limitations in causal inference. Nevertheless, improved measurement technologies and personalized, just-in-time intervention strategies open new opportunities for integrating light exposure into psychiatric research, prevention, and clinical practice.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

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tscnlab/SpitschanEtAl_CurrPsychiatryRep_2025

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Commit: 1ed6dd975ddafd9fef78e58eda48035b08d6ead9, 6 March 2026
Languages: Quarto (2)
Size: 18 files, 2 scripts
Software Heritage: not archived
Found in: “Data Availability”
Holds: 2 notebooks
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: cowplot (2 files), ggplot2 (2 files), patchwork (2 files), tidyverse (2 files)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
2 files

Zenodo 17289456

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Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
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melidosproject/sancho-salasetal_dataset_2025

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: ed90d9ac91b9fa81c0869dafbe6efb3c8d9faed3, 13 May 2026
Languages: Quarto (20), R (2)
Size: 913 files, 22 scripts
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Found in: the Zenodo archive record
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Tools: tidyverse (20 files), cowplot (4 files), patchwork (4 files), ggplot2 (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
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24 files

The paper's code and data availability statement is in the Data section.

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Data

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All code and data are available at https://github.com/tscnlab/SpitschanEtAl_CurrPsychiatryRep_2025.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 6 keywords, 6 MeSH terms, 2 funders, 78 references.

Cite

This paper

Spitschan, M., & Zauner, J. (2026). Light Exposure as a Modifiable Determinant of Mental Health. Current psychiatry reports, 28(1), 24. https://doi.org/10.1007/s11920-026-01671-7

BibTeX

@article{spitschan2026light,
author = {Spitschan, Manuel and Zauner, Johannes},
title = {{Light Exposure as a Modifiable Determinant of Mental Health}},
journal = {Current psychiatry reports},
year = {2026},
month = apr,
volume = {28},
number = {1},
pages = {24},
publisher = {Springer Science+Business Media},
issn = {1523-3812},
doi = {10.1007/s11920-026-01671-7},
url = {https://doi.org/10.1007/s11920-026-01671-7},
pmid = {42047992},
pmcid = {PMC13124800}
}

RIS

TY - JOUR
AU - Spitschan, Manuel
AU - Zauner, Johannes
TI - Light Exposure as a Modifiable Determinant of Mental Health
T2 - Current psychiatry reports
J2 - Curr Psychiatry Rep
PY - 2026
DA - 2026/04/28
VL - 28
IS - 1
SP - 24
SN - 1523-3812
PB - Springer Science+Business Media
DO - 10.1007/s11920-026-01671-7
UR - https://doi.org/10.1007/s11920-026-01671-7
LA - en
ER -

CSL-JSON

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"title": "Light Exposure as a Modifiable Determinant of Mental Health",
"container-title": "Current psychiatry reports",
"author": [
{
"family": "Spitschan",
"given": "Manuel"
},
{
"family": "Zauner",
"given": "Johannes"
}
],
"container-title-short": "Curr Psychiatry Rep",
"volume": "28",
"issue": "1",
"page": "24",
"DOI": "10.1007/s11920-026-01671-7",
"PMID": "42047992",
"PMCID": "PMC13124800",
"ISSN": "1523-3812",
"publisher": "Springer Science+Business Media",
"URL": "https://doi.org/10.1007/s11920-026-01671-7",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
28
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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