Source-space EEG alpha activity reveals brain age gaps due to neurodegeneration and disparity.
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- [1] § Methods › BAG estimation ↔ ElasticNet.ipynb, lines 163–202 · score 0.65 · squared error, absolute error, MSE, MAE, metrics, fold
Paper
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The authors' code
Jupyter notebook · 230 lines · 9.3 KB · no license · 1 match
- # %%
- path= 'C:/Users/felip/OneDrive - Universidad San Sebastian/Documentos/Brain/'
- #import sys
- #sys.path.append(path)
- path_= 'C:/Users/felip/OneDrive - Universidad San Sebastian/Documentos/Brain/Alpha_Brain_Clocks/Codigos_Base'
- import sys
- sys.path.append(path_)
- # %% [markdown]
- # # Regresor
- # %%
- from sklearn.linear_model import ElasticNet
- from base_regressor import BaseRegressor
- from Plotter import Plotter
- from skopt.space import Real, Categorical, Integer
- class ElasticNetRegressor(BaseRegressor):
- def __init__(self, save_path=None, scaler=None, params=None, params_space=None, fit_params_search=None, model_params_search=None, fit_params_train=None, model_params_train=None, name_model="ElasticNet"):
- super().__init__(save_path, scaler, params, params_space, fit_params_search, model_params_search, fit_params_train, model_params_train, name_model)
- self.model_ml = ElasticNet
- if params is None:
- self.params = {
- 'alpha': 0.2,
- 'l1_ratio': 0.5, # Proporción de L1 en la regularización
- 'max_iter': 10000,
- # 'tol': 0.001
- }
- if params_space is None:
- self.params_space = {
- 'alpha': Real(0.0001, 0.01, prior='log-uniform'),
- 'l1_ratio': Real( 0.9, 1.0), # Rango de 0 a 1 para la proporción de L1
- 'max_iter': Integer(1000, 10000),
- #'tol': Real(1e-5, 1e-2, prior='log-uniform')
- }
- # %% [markdown]
- # # Instancia de modelos
- # %%
- # from Plotter import Plotter
- from sklearn.preprocessing import MinMaxScaler,StandardScaler
- model_reg = ElasticNetRegressor()
- Plotters = Plotter()
- # Parametros de Plot
- colorset = 'darkorange'
- nameset = 'ElasticNet'
- #parametros de scaler
- #1:sin scaler 2:Zscore 3:MinMax
- Scaler_reg_train=2
- #scaler = MinMaxScaler()
- Scaler_reg = StandardScaler()
- #model_cls = XGBoostClassifier()
- # %%
- features = [ 'IAF_ORB_left', 'TF_ORB_left', 'IAF_SFG_right', 'Low_subj_spec_EPP_HPC_left', 'IAF_MFG_right', 'TF_INS_right', 'IAF_MFG_left', 'IAF_SFG_left', 'TF_ORB_right', 'Low_subj_spec_EPP_OCC_right', 'IAF_ORB_right', 'IAF_IFG_left', 'IAF_IFG_right', 'TF_IFG_right', 'TF_HPC_right', 'IAF_INS_right', 'TF_HPC_left', 'IAF_INS_left', 'IAF_HPC_left', 'IAF_HPC_right', 'IAF_OCC_left', 'Alpha2_canon_RPD_OCC_right', 'Alpha2_canon_EPP_OCC_right', 'IAF_OCC_right', 'Alpha2_canon_EPP_OCC_left', 'Alpha2_canon_RPD_OCC_left', 'Alpha2_canon_EPP_HPC_left', 'Alpha2_canon_RPD_HPC_left', 'Alpha2_canon_RPD_HPC_right', 'Alpha2_canon_EPP_HPC_right', 'Alpha2_canon_RPD_CING_right', 'High_subj_spec_RPD_OCC_right', 'High_subj_spec_EPP_OCC_right', 'High_subj_spec_RPD_HPC_left', 'High_subj_spec_EPP_HPC_left', 'High_subj_spec_EPP_OCC_left', 'High_subj_spec_RPD_OCC_left', 'High_subj_spec_RPD_CING_right', 'High_subj_spec_EPP_CING_right', 'Low_subj_spec_RPD_OCC_right', 'Low_subj_spec_RPD_OCC_left', 'Alpha2_canon_RPD_CING_left', 'Low_subj_spec_RPD_HPC_left', 'Low_subj_spec_RPD_CING_right', 'High_subj_spec_RPD_HPC_right', 'High_subj_spec_EPP_HPC_right', 'Alpha2_canon_EPP_PARIET_left', 'Alpha2_canon_RPD_PARIET_left', 'High_subj_spec_RPD_CING_left', 'High_subj_spec_EPP_CING_left', 'Alpha2_canon_EPP_PARIET_right', 'Alpha2_canon_RPD_PARIET_right', 'Low_subj_spec_RPD_CING_left', 'Low_subj_spec_RPD_HPC_right', 'High_subj_spec_EPP_PARIET_left', 'High_subj_spec_RPD_PARIET_left', 'Low_subj_spec_RPD_PARIET_left', 'High_subj_spec_RPD_PARIET_right', 'High_subj_spec_EPP_PARIET_right', 'Low_subj_spec_RPD_PARIET_right']
- # %%
- len(features)
- # %% [markdown]
- # # Data
- # %%
- import pandas as pd
- import numpy as np
- from sklearn.preprocessing import MinMaxScaler,StandardScaler
- import pickle
- file_path_CN = f'{path}Alpha_Brain_Clocks/Data/CN_freq.xlsx'
- file_path_AD = f'{path}Alpha_Brain_Clocks/Data/AD_freq.xlsx'
- file_path_FTD = f'{path}Alpha_Brain_Clocks/Data/FTD_freq.xlsx'
- file_path_MCI = f'{path}Alpha_Brain_Clocks/Data/MCI_freq.xlsx'
- df_CN = pd.read_excel(file_path_CN)
- df_AD = pd.read_excel(file_path_AD)
- df_FTD = pd.read_excel(file_path_FTD)
- df_MCI = pd.read_excel(file_path_MCI)
- regiones = ["America", "Turquia", "Europa"]
- countrys = ["Chile", "Argentina", "Colombia", "Brasil", "Turquia", "Reino Unido", "Grecia", "Irlanda"]
- df_CN_filtrado = df_CN[(df_CN['Age'] >=50) & (df_CN['Age'] <= 90)].reset_index(drop=True)
- df_CN_filtrado = df_CN_filtrado[df_CN_filtrado["Region"].isin(regiones)] # Se saca Turquia
- df_AD_filtrado = df_AD[(df_AD['Age'] >= 50) & (df_AD['Age'] <= 90)].reset_index(drop=True)
- df_FTD_filtrado = df_FTD[(df_FTD['Age'] >= 50) & (df_FTD['Age'] <= 90)].reset_index(drop=True)
- df_MCI_filtrado = df_MCI[(df_MCI['Age'] >= 50) & (df_MCI['Age'] <= 90)].reset_index(drop=True)
- # %%
- X_CN = df_CN_filtrado[features]
- y_CN = df_CN_filtrado["Age"]
- ID_CN = df_CN_filtrado["ID_unique"]
- X_AD = df_AD_filtrado[features]
- y_AD = df_AD_filtrado["Age"]
- ID_AD = df_AD_filtrado["ID_unique"]
- X_FTD = df_FTD_filtrado[features]
- y_FTD = df_FTD_filtrado["Age"]
- ID_FTD = df_FTD_filtrado["ID_unique"]
- X_MCI = df_MCI_filtrado[features]
- y_MCI = df_MCI_filtrado["Age"]
- ID_MCI = df_MCI_filtrado["ID_unique"]
- # %%
- scaler = StandardScaler()
- scaler.fit(X_CN)
- X_CN_scaled = scaler.transform(X_CN)
- X_CN_scaled = pd.DataFrame(X_CN_scaled, columns=X_CN.columns)
- df_concatenado_CN = pd.concat([X_CN, y_CN, ID_CN], axis=1, ignore_index=False)
- df_concatenado_AD = pd.concat([X_AD, y_AD, ID_AD], axis=1, ignore_index=False)
- df_concatenado_FTD = pd.concat([X_FTD, y_FTD, ID_FTD], axis=1, ignore_index=False)
- df_concatenado_MCI = pd.concat([X_MCI, y_MCI, ID_MCI], axis=1, ignore_index=False)
- # %% [markdown]
- # # Busqueda Hiperparametros
- # %%
- opt_model, best_params = model_reg.search_best_model (X=X_CN_scaled, y=y_CN, n_iter_=50, scoring_metric='r2')
- # %%
- best_params_ = model_reg.best_hyper(num_best=10, opt_model=opt_model, num_max=50)
- best_params_
- # %% [markdown]
- # # Train
- # %%
- results_labels_df_CN_train, results_labels_df_CN_test, results_model, results_per_fold_CN_train, results_per_fold_CN_test, df_CN_avg_train,df_CN_avg_test= model_reg.trainer(
- X=X_CN,
- y=y_CN,
- ID_label='ID-unique',
- ID=ID_CN,
- n_splits=10,
- n_iterations=20,
- params_=best_params_[0]
- )
- # %%
- results_labels_df_AD_test, results_per_fold_AD_test, df_AD_avg_test = model_reg.test(X=X_AD, y=y_AD, ID= ID_AD, ID_label='ID_unique', n_splits=10, n_iterations=20,result_model=results_model)
- results_labels_df_FTD_test, results_per_fold_FTD_test, df_FTD_avg_test = model_reg.test(X=X_FTD, y=y_FTD, ID= ID_FTD, ID_label='ID_unique', n_splits=10, n_iterations=20,result_model=results_model)
- results_labels_df_MCI_test, results_per_fold_MCI_test, df_MCI_avg_test = model_reg.test(X=X_MCI, y=y_MCI, ID= ID_MCI, ID_label='ID_unique', n_splits=10, n_iterations=20,result_model=results_model)
- # %% [markdown]
- # # Metrics
- # %%
- import pandas as pd
- from sklearn.metrics import mean_absolute_error, mean_squared_error, r2_score
- import numpy as np
- def calculate_metrics(results_per_fold):
- metrics_results = []
- for fold_idx, fold_data in enumerate(results_per_fold):
- y_true = fold_data['y_labels']
- y_pred = fold_data['y_pred']
- y_pred_corrected = fold_data['y_pred_corrected']
- mae = mean_absolute_error(y_true, y_pred)
- mse = mean_squared_error(y_true, y_pred)
- rmse = np.sqrt(mse)
- r2 = r2_score(y_true, y_pred)
- mae_corrected = mean_absolute_error(y_true, y_pred_corrected)
- mse_corrected = mean_squared_error(y_true, y_pred_corrected)
- rmse_corrected = np.sqrt(mse_corrected)
- r2_corrected = r2_score(y_true, y_pred_corrected)
- metrics_results.append({
- 'fold': fold_idx,
- 'MAE': mae,
- 'R2': r2,
- 'MSE': mse,
- 'RMSE': rmse,
- 'MAE_corrected': mae_corrected,
- 'R2_corrected': r2_corrected,
- 'MSE_corrected': mse_corrected,
- 'RMSE_corrected': rmse_corrected
- })
- metrics_df = pd.DataFrame(metrics_results)
- return metrics_df
- # %%
- metrics_df_CN_test = calculate_metrics(results_per_fold_CN_test)
- metrics_df_CN_train = calculate_metrics(results_per_fold_CN_train)
- metrics_df_AD_test = calculate_metrics(results_per_fold_AD_test)
- metrics_df_FTD_test = calculate_metrics(results_per_fold_FTD_test)
- metrics_df_MCI_test = calculate_metrics(results_per_fold_MCI_test)
- # %% [markdown]
- # # SHAP
- # %%
- shap_values_CN, shap_values_avg_CN, shap_summary_sorted_CN, shap_per_fold_CN = model_reg.calculate_multiple_shap(
- df_concatenado_CN, df_concatenado_CN,'ID_unique', results_per_fold_CN_train, results_per_fold_CN_test, results_model['model'],scaler=Scaler_reg_train
- )
- shap_values_AD, shap_values_avg_AD, shap_summary_sorted_AD, shap_per_fold_AD = model_reg.calculate_multiple_shap(
- df_concatenado_CN, df_concatenado_AD,'ID_unique', results_per_fold_CN_train, results_per_fold_AD_test, results_model['model'],scaler=Scaler_reg_train
- )
- shap_values_FTD, shap_values_avg_FTD, shap_summary_sorted_FTD, shap_per_fold_FTD = model_reg.calculate_multiple_shap(
- df_concatenado_CN, df_concatenado_FTD,'ID_unique', results_per_fold_CN_train, results_per_fold_FTD_test, results_model['model'],scaler=Scaler_reg_train
- )
- shap_values_MCI, shap_values_avg_MCI, shap_summary_sorted_MCI, shap_per_fold_MCI = model_reg.calculate_multiple_shap(
- df_concatenado_CN, df_concatenado_MCI,'ID_unique', results_per_fold_CN_train, results_per_fold_MCI_test, results_model['model'],scaler=Scaler_reg_train
- )
ElasticNet.ipynb at commit fffe71c, no license · at the source
Overview
and 22 other authors
Ebru Yıldırım24,25, Lütfü Hanoğlu26, Renato Anghinah27, Pedro A. Valdes-Sosa28,29, Ronaldo Garcia-Reyes28,29, Javier Escudero30, Susanna Lopez31, Robert Whelan9,11, Alberto Fernández32, Adolfo M. García8,10,11,33, David Huepe34, Marcio Soto-Añari35, Eduar Herrera36, Daniel Abasolo37, Nicolás Rubido38, Ruaridh A. Clark39, Wael El-Deredy40, Jesús M. Cortes4, Mario A. Parra41, Claudio Babiloni31,42, Agustin Ibanez3,8,10,11,19,43,44, Pavel Prado4545 affiliations
- Facultad de Ingeniería, Universidad San Sebastián,Santiago, Chile
- Doctorado en Biología Computacional, Universidad San Sebastián,Santiago, Chile
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez,Santiago, Chile
- Computational Neuroimaging Lab, Biobizkaia Health Research Institute, Barakaldo, Spain
- Pontificia Universidad Javeriana, PhD Program of Neuroscience,Bogotá, Colombia
- Center for Brain and Cognition, Intellectus, Bogotá, Colombia
- Hospital Universitario San Ignacio, Bogotá, Colombia and Universidad Nacional de Colombia,Bogotá, Colombia
- Cognitive Neuroscience Center, Universidad de San Andrés,Buenos Aires, Argentina
- School of Psychology, Trinity College Dublin,Dublin, Ireland
- Global Brain Health Institute (GBHI), University of California San Francisco,San Francisco, USA
- Global Brain Health Institute (GBHI), Trinity College Dublin,Dublin, Ireland
- Grupo de Neurociencias de Antioquia (GNA), University of Antioquia,Medellín, Colombia
- Department of Psychology, Master Program of Clinical Neuropsychology, Universidad Surcolombiana Neiva,Huila, Colombia
- Universidad Cooperativa de Colombia,Arauca, Colombia
- AG is with the Laboratorio de Neurocognición y Psicofisología, Universidad Surcolombiana,Neiva, Colombia
- Dokuz Eylül University, Medical School, Neurology Department,Izmir, Turkey
- Dokuz Eylül University, Health Sciences Institute, Neuroscience Department,Izmir, Turkey
- Izmir Biomedicine and Genome Center,Izmir, Turkey
- Department of Biophysics, School of Medicine, Istanbul Medipol University,Istanbul, Turkey
- Neuroscience Research Center, Research Institute for Health Sciences and Technologies, SABITA, Istanbul Medipol University,Istanbul, Turkey
- Dokuz Eylül University, Health Sciences Institute, Neuroscience Department,Izmir, Türkiye
- TA is with the Neuroscience Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University,Istanbul, Turkey
- Section Brain Stimulation and Cognition, Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University,Maastricht, The Netherlands
- Neuroscience and Neurotechnology Center of Excellence (NÖROM), Gazi University,Ankara, Türkiye
- Istanbul Medipol University,Istanbul, Turkey
- Department of Neurology, Istanbul Medipol University,Istanbul, Turkey
- Reference Center of Behavioural Disturbances and Dementia, School of Medicine, University of Sao Paulo,Sao Paulo, Brazil
- Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China,Chengdu, China
- Human Brain Mapping Department, Cuban Neuroscience Center,Habana, Cuba
- Institute for Imaging, Data and Communications, School of Engineering, University of Edinburgh,Edinburgh, UK
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome,Rome, Italy
- Department of Legal Medicine, Psychiatry and Pathology, Complutense University,Madrid, Spain
- Departamento de Lingüística y Literatura, Facultad de Humanidades, Universidad de Santiago,Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibáñez, Penalolen,Santiago, Chile
- Universidad Católica San Pablo,Arequipa, Perú
- Departamento de Estudios Psicológicos, Universidad Icesi,Cali, Colombia
- Centre for Biomedical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Surrey,Guildford, UK
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen,Aberdeen, UK
- Centre for Signal and Image Processing, Department of Electronic and Electrical Engineering, University of Strathclyde,Strathclyde, UK
- Center of Interdisciplinary Biomedical and Engineering Research for Health, Universidad de Valparaíso,Valparaíso, Chile
- Department of Psychological Sciences and Health, University of Strathclyde,Glasgow, UK
- Hospital San Raffaele Cassino, Cassino, Italy
- Trinity College Dublin, The University of Dublin,Dublin, Ireland
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation,Barcelona, Spain
- Escuela de Fonoaudiología, Facultad de Ciencias de la Rehabilitación y Calidad de Vida, Universidad San Sebastián,Santiago, Chile
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.
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CompNeuroLabUSS/Alpha_Brain_Clocks
fffe71c5bf3595f3fb044eae2ce3d1e04f020cda, 27 March 2026Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
2 files
- ElasticNet.ipynb, Jupyter, 230 lines, 1 match
- base_regressor.py, Python, 461 lines
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Alpha_Brain_Clocks
Read it in the paper: doi.org/10.1038/s42003-026-10205-z.
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Data
Datasets cited
- figshare:31918965, at figshare; found in the references
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Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 42 authors, 2 keywords, 14 MeSH terms, 9 funders, 92 references.
Cite
This paper
Otero, M., Carriel-Rubilar, F. I., Hernandez, H., Cuadros, J., Condado, J. G., Sainz-Ballesteros, A., Santamaria-Garcia, H., Legaz, A., Birba, A., Fittipaldi, S., Lopera, F., Ochoa-Gómez, J., Aguillon, D., González-Hernández, A., Bonilla-Santos, J., Gonzalez-Montealegre, R. A., Yener, G. G., Güntekin, B., Kıyı, İ., . . . Prado, P. (2026). Source-space EEG alpha activity reveals brain age gaps due to neurodegeneration and disparity. Communications biology, 9(1), 740. https://
BibTeX
@article{otero2026source
author = {Otero, Mónica and Carriel-Rubilar, Felipe I. and Hernandez, Hernan and Cuadros, Jhosmary and Condado, Jorge G. and Sainz-Ballesteros, Agustin and Santamaria-Garcia, Hernando and Legaz, Agustina and Birba, Agustina and Fittipaldi, Sol and Lopera, Francisco and Ochoa-Gómez, John and Aguillon, David and González-Hernández, Alfredis and Bonilla-Santos, Jasmin and Gonzalez-Montealegre, Rodrigo A. and Yener, Görsev G. and Güntekin, Bahar and Kıyı, İlayda and Aktürk, Tuba and Yıldırım, Ebru and Hanoğlu, Lütfü and Anghinah, Renato and Valdes-Sosa, Pedro A. and Garcia-Reyes, Ronaldo and Escudero, Javier and Lopez, Susanna and Whelan, Robert and Fernández, Alberto and García, Adolfo M. and Huepe, David and Soto-Añari, Marcio and Herrera, Eduar and Abasolo, Daniel and Rubido, Nicolás and Clark, Ruaridh A. and El-Deredy, Wael and Cortes, Jesús M. and Parra, Mario A. and Babiloni, Claudio and Ibanez, Agustin and Prado, Pavel},
title = {{Source-space EEG alpha activity reveals brain age gaps due to neurodegeneration and disparity}},
journal = {Communications biology},
year = {2026},
month = may,
volume = {9},
number = {1},
pages = {740},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/
url = {https://
pmid = {42162258},
pmcid = {PMC13226700}
}
RIS
TY - JOUR
AU - Otero, Mónica
AU - Carriel-Rubilar, Felipe I.
AU - Hernandez, Hernan
AU - Cuadros, Jhosmary
AU - Condado, Jorge G.
AU - Sainz-Ballesteros, Agustin
AU - Santamaria-Garcia, Hernando
AU - Legaz, Agustina
AU - Birba, Agustina
AU - Fittipaldi, Sol
AU - Lopera, Francisco
AU - Ochoa-Gómez, John
AU - Aguillon, David
AU - González-Hernández, Alfredis
AU - Bonilla-Santos, Jasmin
AU - Gonzalez-Montealegre, Rodrigo A.
AU - Yener, Görsev G.
AU - Güntekin, Bahar
AU - Kıyı, İlayda
AU - Aktürk, Tuba
AU - Yıldırım, Ebru
AU - Hanoğlu, Lütfü
AU - Anghinah, Renato
AU - Valdes-Sosa, Pedro A.
AU - Garcia-Reyes, Ronaldo
AU - Escudero, Javier
AU - Lopez, Susanna
AU - Whelan, Robert
AU - Fernández, Alberto
AU - García, Adolfo M.
AU - Huepe, David
AU - Soto-Añari, Marcio
AU - Herrera, Eduar
AU - Abasolo, Daniel
AU - Rubido, Nicolás
AU - Clark, Ruaridh A.
AU - El-Deredy, Wael
AU - Cortes, Jesús M.
AU - Parra, Mario A.
AU - Babiloni, Claudio
AU - Ibanez, Agustin
AU - Prado, Pavel
TI - Source-space EEG alpha activity reveals brain age gaps due to neurodegeneration and disparity
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/
VL - 9
IS - 1
SP - 740
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "Source-space EEG alpha activity reveals brain age gaps due to neurodegeneration and disparity",
"container-title": "Communications biology",
"author": [
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"family": "Otero",
"given": "Mónica"
},
{
"family": "Carriel-Rubilar",
"given": "Felipe I."
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{
"family": "Hernandez",
"given": "Hernan"
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{
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},
{
"family": "Condado",
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"given": "Agustin"
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{
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"given": "Hernando"
},
{
"family": "Legaz",
"given": "Agustina"
},
{
"family": "Birba",
"given": "Agustina"
},
{
"family": "Fittipaldi",
"given": "Sol"
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{
"family": "Lopera",
"given": "Francisco"
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{
"family": "Ochoa-Gómez",
"given": "John"
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{
"family": "Aguillon",
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{
"family": "González-Hernández",
"given": "Alfredis"
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{
"family": "Bonilla-Santos",
"given": "Jasmin"
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{
"family": "Gonzalez-Montealegre",
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"family": "Yener",
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{
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{
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{
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{
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{
"family": "Cortes",
"given": "Jesús M."
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{
"family": "Parra",
"given": "Mario A."
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{
"family": "Babiloni",
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{
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"volume": "9",
"issue": "1",
"page": "740",
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"publisher": "Nature Publishing Group",
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"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
21
]
]
}
}
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