Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions.
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The authors' code
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- ---
- title: "Mikhuna Analysis"
- author: "Gifty Aboagye-Mensah"
- date: "`r Sys.Date()`"
- output: html_document
- ---
- #Dataset upload
- ```{r}
- library(openxlsx)
- Mikhunawide <- read.xlsx(
- file.path("data", "Mikhuna data_OSF.xlsx")
- )
- ```
- #Subsetting dataset
- ```{r}
- library(tidyverse)
- Mikhunafood<- Mikhunawide%>%
- dplyr::select( "record_id", w12_grupo, w35_arroz_blanco, w35_pan_tienda, w35_pan_dulce,
- w35_pan_agua, w35_pan_rodajas_blanco, w35_pan_rodajas_integral,
- w35_fideos_tallerin, w35_fideos_queso, w35_lasana, w35_tortilla,
- w35_granola, w35_quinoa, w35_arroz_cebada, w35_papas_cocinadas,
- w35_papas_fritas, w35_papas_locro, w35_yuca_frita, w35_yuca_cocinada,
- w35_mellocos, w35_oca, w35_camote, w35_choclo, w35_mote, w35_morocho,
- w35_canguil, w35_tostado, w35_platano_verde, w35_platano_maduro,
- w35_sambo, w35_zapallo, w35_menestra_frejol, w35_menestra_lentejas,
- w35_habas_tierna, w35_habas_seca, w35_habas_fritas, w35_chocho,
- w35_garbanzo, w35_alverjas_tierna, w35_alverjas_seca, w35_huevo_cocinado,
- w35_huevo_frito, w35_huevo_revuelto, w35_leche_vaca_entera,
- w35_leche_funda_entera, w35_leche_semidescremada, w35_leche_descremada,
- w35_leche_polvo, w35_nata, w35_cremas_leche, w35_batida_leche,
- w35_yogurt_frutas, w35_yogurt_natural, w35_yogurt_descremada,
- w35_empanada_queso, w35_queso_fresco, w35_queso_mozzarella,
- w35_queso_maduro, w35_mantequilla_sal, w35_mantequilla_sin_sal,
- w35_margarina, w35_res_frita, w35_res_asada_plancha, w35_res_jugo,
- w35_carne_molida, w35_sopa_legumbres_carne, w35_caldo_patas,
- w35_caldo_huesos, w35_pollo_frito, w35_pollo_asado_plancha, w35_pollo_jugo,
- w35_caldo_pollo, w35_pato_pavo, w35_cerdo, w35_borrego, w35_ternero,
- w35_menudencia, w35_higado_animal, w35_cerebro_animal, w35_sangre_frita,
- w35_salchicha, w35_mortadela_jamon, w35_pescado_frito, w35_pescado_asado,
- w35_pescado_envuelto, w35_sopa_pescado, w35_atun_aceite, w35_atun_agua,
- w35_sardinas, w35_camarones, w35_conchas, w35_cangrejo, w35_calamar,
- w35_pulpo, w35_empanada_carne, w35_empanada_pollo,
- w35_pescado_frito_tipo___1, w35_pescado_frito_tipo___2, w35_pescado_frito_tipo___3,
- w35_pescado_frito_tipo___4, w35_pescado_frito_tipo___5, w35_pescado_frito_tipo___77,
- w35_pescado_frito_especifique, w35_pescado_asado_tipo___1, w35_pescado_asado_tipo___2,
- w35_pescado_asado_tipo___3, w35_pescado_asado_tipo___4, w35_pescado_asado_tipo___5,
- w35_pescado_asado_especifique, w35_pescado_envuelto_tipo___1, w35_pescado_envuelto_tipo___2,
- w35_pescado_envuelto_tipo___3, w35_pescado_envuelto_tipo___4, w35_pescado_envuelto_tipo___5,
- w35_pescado_envuelto_tipo___77, w35_pescado_envuelto_especif, w35_guineo,
- w35_manzana, w35_pera, w35_pina, w35_papaya, w35_melon, w35_sandia, w35_naranja,
- w35_mandarina, w35_limon, w35_lima, w35_toronja, w35_uvas, w35_durazno,
- w35_kiwi, w35_mora, w35_arandano, w35_mortino, w35_frutillas_fresas,
- w35_uvilla, w35_mango, w35_tomate_arbol, w35_frutas_secas, w35_pasas,
- w35_ciruela, w35_aguacate, w35_taxo, w35_granadilla, w35_tuna, w35_naranjilla,
- w35_maracuya, w35_guanabana, w35_chirimoya, w35_guayaba, w35_guaba, w35_babaco,
- w35_pepinillo_dulce, w35_tamarindo, w35_pitahaya, w35_zapote, w35_nueces,
- w35_almendra, w35_mani, w35_mani_tostado, w35_mani_pasta, w35_tocte,
- w35_tomate_rinon, w35_tomate_cherry, w35_zanahoria, w35_rabanos, w35_brocoli,
- w35_coliflor, w35_pepinillo, w35_remolacha, w35_vainitas, w35_berenjenas,
- w35_esparragos, w35_pepino, w35_pimiento, w35_cebolla_paitina, w35_cebolla_perla,
- w35_cebolla_larga, w35_cebollin, w35_col_blanca, w35_col_morada, w35_lechuga,
- w35_nabo, w35_rucula, w35_kale, w35_acelga, w35_espinaca, w35_alcachofa,
- w35_hongos_ostra, w35_ajo, w35_apio, w35_cilantro, w35_perejil, w35_albahaca_fresca,
- w35_aji, w35_hierba_buena, w35_jengibre, w35_avena_frutas, w35_avena_leche,
- w35_avena_agua, w35_machica_leche, w35_machina_sin_leche, w35_higos_queso,
- w35_salsa_tomate, w35_hamburguesa, w35_pizza, w35_humitas_tamales_quimbolito,
- w35_arepa, w35_mermelada
- )
- ```
- ```{r}
- head(Mikhunafood)
- ```
- #Converting character values to numeric
- ```{r}
- food_cols <- names(Mikhunafood)[!(names(Mikhunafood) %in% c("record_id", "w12_grupo"))]
- Mikhunafood[food_cols] <- lapply(Mikhunafood[food_cols], function(x) as.numeric(as.character(x)))
- ```
- #Viewing first few rows
- ```{r}
- head(Mikhunafood)
- ```
- #Converting from wide to long
- ```{r}
- library(tidyr)
- library(dplyr)
- food_long <- Mikhunafood %>%
- pivot_longer(
- cols = -c(record_id, w12_grupo), # keep group column out
- names_to = "food_var",
- values_to = "consumed"
- )
- ```
- #Viewing long dataset
- ```{r}
- head(food_long)
- ```
- #Importing MDD-W categories as food_map
- ```{r}
- library(tidyr)
- library(dplyr)
- library(readxl)
- food_map <- read_excel("data", "MDD-W food groups")
- ```
- #Viewing food_map
- ```{r}
- head(food_map)
- ```
- ```{r}
- colnames(food_map)
- ```
- #Converting food_map from wide to long
- ```{r}
- food_map_long <- food_map %>%
- pivot_longer(
- cols = starts_with("Category"), # Category 1 … Category 10
- names_to = "cat_number",
- values_to = "MDDW_category"
- ) %>%
- filter(MDDW_category != "") %>% # remove empty category cells
- select(food_var, MDDW_category)
- ```
- ```{r}
- head(food_map_long)
- ```
- #Merging food_map_long and food_long into food_long1
- ```{r}
- food_long1 <- food_long %>%
- left_join(food_map_long, by = "food_var", relationship = "many-to-many")
- ```
- ```{r}
- colnames(food_long1)
- ```
- #Counting participants per category sorted by group. 1- control, 2-intervention
- ```{r}
- category_counts <- food_long1 %>%
- filter(consumed == 1) %>%
- group_by(w12_grupo, MDDW_category) %>%
- summarise(n_participants = n_distinct(record_id), .groups = "drop")
- ```
- ```{r}
- head(category_counts)
- ```
- #Calculating percentages of participants per group who consumes each MDD-W category
- ```{r}
- total_per_group <- food_long1 %>%
- select(record_id, w12_grupo) %>%
- distinct() %>%
- group_by(w12_grupo) %>%
- summarise(total_participants = n())
- category_percent <- category_counts %>%
- left_join(total_per_group, by = "w12_grupo") %>%
- mutate(percent = 100 * n_participants / total_participants)
- ```
- #How many participants consumed each specific food item per group
- #Filtering to leave only foods consumed
- ```{r}
- food_long_consumed <- food_long1 %>%
- filter(consumed == 1)
- ```
- #Counting participants per food group
- ```{r}
- food_counts <- food_long_consumed %>%
- group_by(w12_grupo, food_var) %>%
- summarise(n_participants = n_distinct(record_id), .groups = "drop")
- ```
- #Mapping foods to their MDD-W categories
- ```{r}
- food_counts_with_cat <- food_counts %>%
- left_join(
- food_map_long %>% select(food_var, MDDW_category),
- by = "food_var",
- relationship = "many-to-many"
- )
- ```
- #Total number and percentage of participants that consumed each food per group
- ```{r}
- food_percent <- food_counts %>%
- left_join(total_per_group, by = "w12_grupo") %>%
- mutate(percent = 100 * n_participants / total_participants)
- ```
- #Adding MDD-W category to food_percent
- ```{r}
- food_percent_with_cat <- food_percent %>%
- left_join(
- food_map_long %>% select(food_var, MDDW_category),
- by = "food_var",
- relationship = "many-to-many"
- )
- ```
- #Fixing "grains roots and tubers" variable
- ```{r}
- food_map_long <- food_map_long %>%
- mutate(
- MDDW_category = MDDW_category %>%
- tolower() %>% # lower case
- trimws() %>% # remove leading/trailing spaces
- gsub(",", "", .) %>% # remove commas
- gsub("\\s+", " ", .) %>% # fix multiple spaces
- gsub(" +and +", " and ", .) # normalize 'and'
- )
- ```
- ```{r}
- food_map_long <- food_map_long %>%
- mutate(
- MDDW_category = case_when(
- grepl("grains.*roots.*tubers", MDDW_category) ~ "grains roots and tubers",
- TRUE ~ MDDW_category
- )
- )
- ```
- ```{r}
- food_long_with_cat <- food_long %>%
- left_join(
- food_map_long,
- by = "food_var",
- relationship = "many-to-many"
- )
- ```
- ```{r}
- category_percent <- food_long_with_cat %>%
- group_by(w12_grupo, MDDW_category) %>%
- summarise(
- n_consumed = sum(consumed == 1, na.rm = TRUE),
- total = n_distinct(record_id),
- percent = 100 * n_consumed / total,
- .groups = "drop"
- )
- ```
- #Above results counts foods as numerator and not participants.
- #Fixing so that numerator is number of participants
- ```{r}
- category_binary <- food_long_with_cat %>%
- filter(consumed == 1) %>%
- group_by(record_id, w12_grupo, MDDW_category) %>%
- summarise(any_consumed = 1, .groups = "drop")
- ```
- ```{r}
- category_counts <- category_binary %>%
- count(w12_grupo, MDDW_category, name = "n_consumed")
- ```
- ```{r}
- total_per_group <- food_long_with_cat %>%
- distinct(record_id, w12_grupo) %>%
- count(w12_grupo, name = "total_per_group")
- ```
- ```{r}
- category_percents <- category_counts %>%
- left_join(total_per_group, by = "w12_grupo") %>%
- mutate(percent = 100 * n_consumed / total_per_group)
- ```
- #Exporting tables
- ```{r}
- library(openxlsx)
- # Save to Desktop (change username if needed)
- write.xlsx(
- list(
- "Food_Percent_With_Categories" = food_percent_with_cat,
- "Category_Percents" = category_percents
- ),
- file = "C:/Users/Gifty Aboagye-Mensah/Desktop/Mikhuna_Food_Results.xlsx"
- )
- ```
- #Calculating chi-squares
- ```{r}
- class(category_percents)
- ```
- ```{r}
- class(category_percents)
- class(group_by)
- class(mutate)
- ```
- ```{r}
- results <- category_percents %>%
- mutate(
- not_consumed = total_per_group - n_consumed
- ) %>%
- group_by(MDDW_category) %>%
- group_modify(~{
- # extract values for each group
- c_yes <- .x$n_consumed[.x$w12_grupo == 1]
- c_no <- .x$not_consumed[.x$w12_grupo == 1]
- i_yes <- .x$n_consumed[.x$w12_grupo == 2]
- i_no <- .x$not_consumed[.x$w12_grupo == 2]
- # construct contingency table
- tbl <- matrix(c(c_yes, c_no, i_yes, i_no), nrow = 2, byrow = TRUE)
- # chi-squared test
- test <- chisq.test(tbl, correct = FALSE)
- tibble(
- control_percent = .x$percent[.x$w12_grupo == 1],
- intervention_percent = .x$percent[.x$w12_grupo == 2],
- p_value = test$p.value
- )
- }) %>%
- ungroup()
- ```
- #Calculating MDD_W scores per participant
- ```{r}
- category_binary <- food_long_with_cat %>%
- filter(consumed == 1) %>% # keep only foods consumed
- group_by(record_id, w12_grupo, MDDW_category) %>%
- summarise(any_consumed = 1, .groups = "drop")
- mddw_score <- category_binary %>%
- group_by(record_id, w12_grupo) %>%
- summarise(
- MDDW_score = sum(any_consumed),
- .groups = "drop"
- )
- ```
- #For all participants even those who consumed 0 food groups
- ```{r}
- all_participants <- food_long_with_cat %>%
- distinct(record_id, w12_grupo)
- mddw_score_full <- all_participants %>%
- left_join(mddw_score, by = c("record_id", "w12_grupo")) %>%
- mutate(MDDW_score = replace_na(MDDW_score, 0))
- ```
- #Adding 0/1 code for MDD-W
- ```{r}
- mddw_score_full <- mddw_score_full %>%
- mutate(
- MDDW_indicator = if_else(MDDW_score >= 5, 1, 0)
- )
- ```
- #Summary statistics for each group
- ```{r}
- mddw_summary <- mddw_score_full %>%
- group_by(w12_grupo) %>%
- summarise(
- mean_score = mean(MDDW_score),
- sd_score = sd(MDDW_score),
- n_participants = n(),
- n_meeting_MDDW = sum(MDDW_indicator),
- percent_meeting_MDDW = 100 * mean(MDDW_indicator),
- .groups = "drop"
- )
- ```
- #Crearing 2x2 contingency table
- ```{r}
- # Contingency table: rows = group, columns = MDDW indicator
- table_mddw <- table(
- Group = mddw_score_full$w12_grupo,
- MDDW = mddw_score_full$MDDW_indicator
- )
- table_mddw
- ```
- #Chi square test
- ```{r}
- chi_result <- chisq.test(table_mddw, correct = FALSE) # no Yates' correction
- chi_result
- ```
- #Calculating species richness
- ```{r}
- species_richness <- food_long_with_cat %>%
- filter(consumed == 1) %>% # keep only foods eaten
- group_by(record_id, w12_grupo) %>%
- summarise(
- richness = n_distinct(food_var),
- .groups = "drop"
- )
- head(species_richness)
- ```
- #Merging for all participants (include NA for participants with no data)
- ```{r}
- species_richness_full <- all_participants %>%
- left_join(species_richness, by = c("record_id", "w12_grupo")) %>%
- mutate(richness = replace_na(richness, 0))
- ```
- #Adding species richness to MDD-W score data
- ```{r}
- mddw_with_richness <- mddw_score_full %>%
- left_join(species_richness_full, by = c("record_id", "w12_grupo"))
- head(mddw_with_richness)
- ```
- #Testing for equality of variances
- ```{r}
- library(car)
- leveneTest(richness ~ as.factor(w12_grupo), data = species_richness_full)
- ```
- #Welch's t-test
- ```{r}
- t_test_richness <- t.test(
- richness ~ w12_grupo,
- data = species_richness_full,
- var.equal = FALSE # Welch t-test
- )
- t_test_richness
- ```
- #Equal variance (pooled) t-test
- ```{r}
- t_test_richness_equalvar <- t.test(
- richness ~ w12_grupo,
- data = species_richness_full,
- var.equal = TRUE
- )
- t_test_richness_equalvar
- ```
- ```{r}
- species_richness_full %>%
- group_by(w12_grupo) %>%
- summarise(
- n = n(),
- mean_richness = mean(richness, na.rm = TRUE),
- sd_richness = sd(richness, na.rm = TRUE)
- )
- ```
MikhunaMDD-W.Rmd, no license · at the source
Overview
- E3 Nutrition Lab, Bursky School of Public Health, Washington University in St. Louis, St. Louis, MO 63130
- Institute for Research in Health and Nutrition, Universidad San Francisco de Quito, Quito 170902, Ecuador
- Q*RA Medicina Especialidades, Quito 170184, Ecuador
- Amazonic Gardens, Quito 170902, Ecuador
- Institute for Agroecology, University of Vermont, Burlington, VT 05405
- Rollins School of Public Health, Emory University, Atlanta, GA 30322
- Bursky School of Public Health, Washington University in St. Louis, St. Louis, MO 63130
- Neuroimaging Labs Research Center, Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
- Department of Radiology, University of Colorado School of Medicine, Aurora, CO 80045
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.
Repository
Its files are read in the Code ↔ Paper reader above.
OSF qwap8
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
1 file
- MikhunaMDD-W.Rmd, R, 495 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;
- 1 script, each with its path and the digest of its content;
- no match between paragraphs and code yet;
- 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.
Code and data availability statement
The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- no repository, dataset or request procedure was recognized in it
Read it in the paper: doi.org/10.1073/pnas.2602218123.
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, issue, pages, dates, 18 authors, 5 keywords, 11 MeSH terms, 1 funder, 56 references.
Cite
This paper
Iannotti, L. L., Vintimilla Andrade, G., Tipanquiza Piedra, S., Zimmerman, R. B., Hahn, E., Camana, P., Baldeon, D., Silva, P., Balladares, K., Gallegos-Riofrio, C. A., Chapnick, M., Aboagye-Mensah, G., Zielonko, T., Raichle, M., Goyal, M. S., Waters, W. F., Palacios León, I., & Nicholas, J. (2026). Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions. Proceedings of the National Academy of Sciences of the United States of America, 123(36), e2602218123. https://
BibTeX
@article{iannotti2026pre
author = {Iannotti, Lora L. and Vintimilla Andrade, Gabriela and Tipanquiza Piedra, Shirley and Zimmerman, Rachel B. and Hahn, Elizabeth and Camana, Pamela and Baldeon, Dessire and Silva, Paul and Balladares, Karen and Gallegos-Riofrio, Carlos Andres and Chapnick, Melissa and Aboagye-Mensah, Gifty and Zielonko, Timothy and Raichle, Marcus and Goyal, Manu S. and Waters, William F. and Palacios León, Iván and Nicholas, Jennifer},
title = {{Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = aug,
volume = {123},
number = {36},
pages = {e2602218123},
publisher = {National Academy of Sciences},
issn = {0027-8424},
doi = {10.1073/
url = {https://
pmid = {42673450},
pmcid = {PMC13552917}
}
RIS
TY - JOUR
AU - Iannotti, Lora L.
AU - Vintimilla Andrade, Gabriela
AU - Tipanquiza Piedra, Shirley
AU - Zimmerman, Rachel B.
AU - Hahn, Elizabeth
AU - Camana, Pamela
AU - Baldeon, Dessire
AU - Silva, Paul
AU - Balladares, Karen
AU - Gallegos-Riofrio, Carlos Andres
AU - Chapnick, Melissa
AU - Aboagye-Mensah, Gifty
AU - Zielonko, Timothy
AU - Raichle, Marcus
AU - Goyal, Manu S.
AU - Waters, William F.
AU - Palacios León, Iván
AU - Nicholas, Jennifer
TI - Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions
T2 - Proceedings of the National Academy of Sciences of the United States of America
J2 - Proc Natl Acad Sci U S A
PY - 2026
DA - 2026/
VL - 123
IS - 36
SP - e2602218123
SN - 0027-8424
PB - National Academy of Sciences
DO - 10.1073/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1073/
"type": "article-journal",
"title": "Pregnancy diet based on ancestral patterns increases growth in subcortical fetal brain regions",
"container-title": "Proceedings of the National Academy of Sciences of the United States of America",
"author": [
{
"family": "Iannotti",
"given": "Lora L."
},
{
"family": "Vintimilla Andrade",
"given": "Gabriela"
},
{
"family": "Tipanquiza Piedra",
"given": "Shirley"
},
{
"family": "Zimmerman",
"given": "Rachel B."
},
{
"family": "Hahn",
"given": "Elizabeth"
},
{
"family": "Camana",
"given": "Pamela"
},
{
"family": "Baldeon",
"given": "Dessire"
},
{
"family": "Silva",
"given": "Paul"
},
{
"family": "Balladares",
"given": "Karen"
},
{
"family": "Gallegos-Riofrio",
"given": "Carlos Andres"
},
{
"family": "Chapnick",
"given": "Melissa"
},
{
"family": "Aboagye-Mensah",
"given": "Gifty"
},
{
"family": "Zielonko",
"given": "Timothy"
},
{
"family": "Raichle",
"given": "Marcus"
},
{
"family": "Goyal",
"given": "Manu S."
},
{
"family": "Waters",
"given": "William F."
},
{
"family": "Palacios León",
"given": "Iván"
},
{
"family": "Nicholas",
"given": "Jennifer"
}
],
"container-title-short":
"volume": "123",
"issue": "36",
"page": "e2602218123",
"DOI": "10.1073/
"PMID": "42673450",
"PMCID": "PMC13552917",
"ISSN": "0027-8424",
"publisher": "National Academy of Sciences",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
31
]
]
}
}
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