Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis.
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- [1] § Materials and methods › Receptor preparation ↔ Receptor Preparation and Structure-based Screeening.ipynb, lines 166 to 211 · score 0.71 · PDBFixer, missing atoms, hydrogen, residues, AlphaFold, Receptor · Report a mismatch
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The authors' code
Jupyter notebook · 493 lines · 14 KB · no license · 1 match
- # %% [markdown]
- # # Data preparation
- # %% [markdown]
- # ## download af structures via uniport id
- # %%
- import pandas as pd
- file = pd.read_csv('data/2_Autophagy_OR_Mitophagy.csv')
- print(file.shape)
- file = file.rename(columns={'Uniprot ID':'Uniprot'})
- file.head(2)
- # %%
- import requests
- from pathlib import Path
- from tqdm import tqdm
- ids = file.Uniprot.tolist()
- error_list = []
- output_dir = Path("alphafold_mouse")
- output_dir.mkdir(exist_ok=True)
- for uniprot_id in tqdm(ids):
- url = f"https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-model_v6.pdb"
- out_path = output_dir / f"AF-{uniprot_id}-F1-model_v4.pdb"
- #print(f"Downloading {uniprot_id} ...")
- try:
- r = requests.get(url, timeout=10)
- r.raise_for_status()
- out_path.write_bytes(r.content)
- except Exception as e:
- print(f"Failed to download {uniprot_id}: {e}")
- error_list.append(uniprot_id)
- # %%
- ids = file.Uniprot.tolist()
- # %%
- import os
- import pandas as pd
- dir_path = 'alphafold_mouse'
- filenames = [f for f in os.listdir(dir_path) if os.path.isfile(os.path.join(dir_path, f))]
- df = pd.DataFrame(filenames, columns=['filename'])
- print(df.shape)
- df.head()
- # %%
- # %%
- df['name'] = df["filename"].str.split("-").str[1]
- ids_df = pd.DataFrame(ids, columns=["name"])
- print(ids_df.shape)
- ids_df = ids_df[~ids_df.name.isin(df['name'])]
- print(ids_df.shape)
- # %%
- df.to_csv('data/downloaded_AFpdb.csv',index=False)
- # %%
- ids_df.to_csv('data/missing_AFpdb.csv',index=False)
- # %%
- ids_df.shape
- # %% [markdown]
- # # Pocket prediction and fliter
- # %% [markdown]
- # ## use p2rank to seg pockets
- # %%
- import pandas as pd
- # %%
- df = pd.read_csv('data/downloaded_AFpdb.csv')
- # %%
- ds = f"protein_list.ds"
- with open(ds, "w") as out:
- for i in df.filename:
- out.write(f"alphafold_mouse/{i}\n")
- # %%
- shutil.unpack_archive('p2rank_23_archive.zip', 'p2rank_23')
- # %%
- import os
- import time
- start_time = time.time()
- p2rank = "p2rank_23/prank"
- cmd = f"{p2rank} predict {ds} -o af_workspace1/p2rank -threads 64"
- os.system(cmd)
- # Record end time
- end_time = time.time()
- # Calculate elapsed time
- p2rank_time = end_time - start_time
- # %%
- print(p2rank_time)
- # %% [markdown]
- # ## fliter none pocket proteins
- # %%
- import pandas as pd
- tmp = pd.read_csv("af_workspace/p2rank/AF-Q14005-F1-model_v4.pdb_predictions.csv")
- print(tmp[[' center_x', ' center_y', ' center_z']])
- tmp.head(2)
- # %%
- import pandas as pd
- import os
- import re
- from tqdm import tqdm
- workspace = "af_workspace/p2rank"
- non_empty_ids = []
- matching_files = [f for f in os.listdir(workspace) if re.match(r'AF-.+-F1-model_v4\.pdb_predictions\.csv', f)]
- matching_files.sort()
- for filename in tqdm(matching_files, desc="Checking files", unit="file"):
- match = re.match(r'AF-(.+)-F1-model_v4\.pdb_predictions\.csv', filename)
- if match:
- file_id = match.group(1)
- file_path = os.path.join(workspace, filename)
- try:
- df = pd.read_csv(file_path)
- if len(df) > 0:
- non_empty_ids.append(file_id)
- except pd.errors.EmptyDataError:
- continue
- result_df = pd.DataFrame({"non_empty_ids": non_empty_ids})
- print(f"Found {len(non_empty_ids)} non-empty files")
- # %%
- result_df.to_csv('data/downloaded_AFpdb_wpocket.csv',index=False)
- # %% [markdown]
- # # Docking
- # %% [markdown]
- # ## sample code for docking with predicted pocket info
- # %%
- import pandas as pd
- result_df = pd.read_csv('data/downloaded_AFpdb_wpocket.csv')
- df = pd.read_csv('data/downloaded_AFpdb.csv')
- df = df[df.name.isin(result_df.non_empty_ids)]
- # %%
- import pandas as pd
- from pdbfixer import PDBFixer
- from openmm.app import PDBFile
- from concurrent.futures import ProcessPoolExecutor, as_completed
- from pathlib import Path
- from tqdm import tqdm
- def add_h(protein_file, outpath):
- try:
- fixer = PDBFixer(protein_file)
- fixer.findMissingResidues()
- fixer.findNonstandardResidues()
- fixer.replaceNonstandardResidues()
- fixer.removeHeterogens(True)
- fixer.findMissingAtoms()
- fixer.addMissingAtoms()
- fixer.addMissingHydrogens(7.4)
- with open(outpath, "w") as f:
- PDBFile.writeFile(fixer.topology, fixer.positions, f)
- return (protein_file, True, "")
- except Exception as e:
- return (protein_file, False, str(e))
- def process_file(filename, prep_dir, out_dir):
- protein_path = f"{prep_dir}/{filename}"
- outpath = f"{out_dir}/{filename}"
- return add_h(protein_path, outpath)
- if __name__ == "__main__":
- outpath = 'alphafold_mouse'
- output_dir = Path(outpath)
- output_dir.mkdir(exist_ok=True)
- prep = 'alphafold_mouse'
- filenames = df.filename.tolist()
- # 并行处理
- results = []
- with ProcessPoolExecutor(max_workers=8) as executor:
- futures = [executor.submit(process_file, fname, prep, outpath) for fname in filenames]
- for future in tqdm(as_completed(futures), total=len(futures)):
- result = future.result()
- results.append(result)
- if not result[1]:
- print(f"❌ Failed: {result[0]}\nError: {result[2]}")
- # %%
- import subprocess
- from tqdm import tqdm
- from pathlib import Path
- outpath = 'debug'
- output_dir = Path(outpath)
- output_dir.mkdir(exist_ok=True)
- ligand_o = f'af_workspace/Keto.sdf'
- ligand_h = f'af_workspace/NAce.sdf'
- prep='alphafold_mouse'
- for i in tqdm(df.filename):
- try:
- df1 = pd.read_csv(f'af_workspace/p2rank/{i}_predictions.csv')
- protein_path = f'{prep}/{i}'
- i=i.split("-")[1]
- print(f'start docking {i}')
- out_dict_o = f'{outpath}/{i}/'
- out_dict_h = f'{outpath}/{i}/'
- #add_h(protein_path, protein_path)
- '''for j in range(df.shape[0]):
- x,y,z = df1.loc[j][[' center_x', ' center_y', ' center_z']].values
- subprocess.run(f'unidocktools unidock_pipeline -r {protein_path} -l {ligand_o} -sd {out_dict_o} -nm 10 -cx {x} -cy {y} -cz {z}', shell=True, check=True)
- subprocess.run(f'unidocktools unidock_pipeline -r {protein_path} -l {ligand_h} -sd {out_dict_h} -nm 10 -cx {x} -cy {y} -cz {z}', shell=True, check=True)
- '''
- x,y,z = df1[' center_x'][0],df1[' center_y'][0],df1[' center_z'][0]
- subprocess.run(f'unidocktools unidock_pipeline -r {protein_path} -l {ligand_o} -sd {out_dict_o} -nm 25 -cx {x} -cy {y} -cz {z}', shell=True, check=True)
- subprocess.run(f'unidocktools unidock_pipeline -r {protein_path} -l {ligand_h} -sd {out_dict_h} -nm 25 -cx {x} -cy {y} -cz {z}', shell=True, check=True)
- except Exception as e:
- print(e)
- print(i)
- # %%
- import tempfile
- import os
- import shutil
- def filter_pdb(input_file, output_file=None):
- if output_file is None or input_file == output_file:
- input_dir = os.path.dirname(os.path.abspath(input_file))
- temp_fd, temp_path = tempfile.mkstemp(
- suffix='.pdb',
- dir=input_dir
- )
- os.close(temp_fd)
- else:
- temp_path = None
- try:
- with open(input_file, 'r') as infile, open(temp_path or output_file, 'w') as outfile:
- for line in infile:
- if line.startswith(('ATOM', 'TER', 'END')): #, 'CONECT'
- outfile.write(line)
- if temp_path:
- os.replace(temp_path, input_file)
- #print(f"{input_file}")
- finally:
- if temp_path and os.path.exists(temp_path):
- os.remove(temp_path)
- for subdir in tqdm(list(docking_dir.iterdir()), desc="Collecting docking info"):
- if subdir.is_dir():
- pdb_id = subdir.name
- protein_file = protein_dir / f"AF-{pdb_id}-F1-model_v4.pdb"
- #print(protein_file)
- if not protein_file.exists():
- print(f"[Warning] Missing protein file: {protein_file}")
- continue
- filter_pdb(protein_file)
- # %% [markdown]
- # ## prepare ligand config
- # %%
- import pandas as pd
- ligand = pd.read_csv('data/1_first_stage_compound.csv')
- ligand['Source_idx'] = ligand['Source_idx'].astype(str)
- ligand['path'] = "af_workspace/"+ligand.Source_idx+'.sdf'
- print(ligand.shape)
- ligand.head(1)
- # %%
- import pandas as pd
- from rdkit import Chem
- from rdkit.Chem import AllChem, SDWriter
- from tqdm import tqdm
- def smiles_to_individual_sdf(df, smiles_col, name_col, out_dir="./sdf_files"):
- import os
- os.makedirs(out_dir, exist_ok=True)
- for idx, row in tqdm(df.iterrows(), total=len(df)):
- smi = row[smiles_col]
- name = str(row[name_col]) # 用 name_col 来命名
- mol = Chem.MolFromSmiles(smi)
- if mol is None:
- print(smi)
- continue
- mol = Chem.AddHs(mol)
- AllChem.EmbedMolecule(mol, AllChem.ETKDG())
- AllChem.UFFOptimizeMolecule(mol)
- mol_noH = Chem.RemoveHs(mol)
- mol_noH.SetProp("_Name", name)
- file_path = os.path.join(out_dir, f"{name}.sdf")
- with SDWriter(file_path) as writer:
- writer.write(mol_noH)
- #print(f"✅ {name}.sdf saved")
- smiles_to_individual_sdf(ligand, smiles_col="Smiles", name_col="Source_idx", out_dir="./af_workspace")
- # %%
- import os
- import pandas as pd
- folder = "af_workspace"
- sdf_files = [f for f in os.listdir(folder) if f.endswith(".sdf")]
- df1 = pd.DataFrame({"ligand": sdf_files})
- df1['ligand'] = "af_workspace/"+df1['ligand']
- df1.to_csv('data/ligands.csv',index=False, header=None)
- # %%
- import subprocess
- import pandas as pd
- import time
- start = time.time()
- file_path = 'alphafold_mouse/AF-O60356-F1-model_v4.pdb'
- df1 = pd.read_csv(f'af_workspace1/p2rank/AF-A1A4Y4-F1-model_v4.pdb_predictions.csv')
- df1.columns = [col.strip() for col in df1.columns]
- x, y, z = df1.loc[0][['center_x', 'center_y', 'center_z']].values
- x, y, z
- subprocess.run(f'unidock --receptor alphafold_mouse/AF-A1A4Y4-F1-model_v4.pdb --ligand 20883.sdf --search_mode balance --center_x {x} --center_y {y} --center_z {z} --size_x 25 --size_y 25 --size_z 25 --dir tmp', shell=True, check=True)
- end = time.time()
- # %%
- import glob
- import os
- import subprocess
- from tqdm import tqdm
- from pathlib import Path
- import time
- start = time.time()
- for i in tqdm(range(df.shape[0])):#
- file_path = 'alphafold_mouse/'+df.filename.iloc[i]
- df1 = pd.read_csv(f'af_workspace/p2rank/{df.filename.iloc[i]}_predictions.csv')
- df1.columns = [col.strip() for col in df1.columns]
- x, y, z = df1.loc[0][['center_x', 'center_y', 'center_z']].values
- outputdir = f"dock_record/{file_path.split('/')[-1][:-4]}"
- os.makedirs(outputdir, exist_ok=True)
- subprocess.run(f'unidock --receptor {file_path} --ligand_index ligands.csv --search_mode balance --center_x {x} --center_y {y} --center_z {z} --size_x 25 --size_y 25 --size_z 25 --dir {outputdir}', shell=True, check=True)
- base_path = './'
- output_folder = os.path.join(base_path, "files")
- os.makedirs(output_folder, exist_ok=True)
- save_name = f"{file_path.split('/')[-1][:-5]}.txt"
- file_save_path = os.path.join(output_folder, save_name)
- with open(file_save_path, "w", encoding="utf-8") as f:
- f.write('finished')
- end = time.time()
- # %% [markdown]
- # ## Check result
- # %%
- import os
- import glob
- import pandas as pd
- import re
- from concurrent.futures import ProcessPoolExecutor, as_completed
- from tqdm import tqdm
- base_dir = "dock_record"
- def get_target_folders(base_dir):
- pattern = os.path.join(base_dir, "AF-*")
- folders = [f for f in glob.glob(pattern) if os.path.isdir(f)]
- return folders
- def process_folder(folder):
- results = []
- folder_name = os.path.basename(folder)
- try:
- protein_id = folder_name.split('-')[1] # e.g., Q92985
- except IndexError:
- protein_id = "UNKNOWN"
- sdf_files = glob.glob(os.path.join(folder, "*.sdf"))
- for sdf_file in sdf_files:
- try:
- with open(sdf_file, "r") as f:
- content = f.read()
- except Exception as e:
- continue # silent skip or log if needed
- blocks = content.split("$$$$")
- for block in blocks:
- match = re.search(r"> <Uni-Dock RESULT>.*?ENERGY=\s*([-\d\.]+)", block, re.DOTALL)
- if match:
- try:
- energy = float(match.group(1))
- results.append({
- "file": os.path.basename(sdf_file),
- "energy": energy,
- "protein": protein_id,
- "folder": folder_name
- })
- except ValueError:
- pass
- break
- if not results:
- return pd.DataFrame()
- df = pd.DataFrame(results)
- df = df.sort_values(by="energy", ascending=True).reset_index(drop=True)
- df = df.drop_duplicates(subset=["file", "protein"], keep="first").reset_index(drop=True)
- return df
- def main():
- folders = get_target_folders(base_dir)
- print(f"Found {len(folders)} folders to process.")
- if not folders:
- print("No folders found. Check base_dir path.")
- return
- all_dfs = []
- with ProcessPoolExecutor(max_workers=min(16, os.cpu_count())) as executor:
- future_to_folder = {executor.submit(process_folder, folder): folder for folder in folders}
- with tqdm(total=len(future_to_folder), desc="Processing folders") as pbar:
- for future in as_completed(future_to_folder):
- try:
- df = future.result()
- if not df.empty:
- all_dfs.append(df)
- except Exception as e:
- folder = future_to_folder[future]
- print(f"\nError processing {folder}: {e}")
- finally:
- pbar.update(1)
- if all_dfs:
- final_df = pd.concat(all_dfs, ignore_index=True)
- final_df.to_csv("data/merged_docking_results1.csv", index=False)
- print(f"\n✅ Saved merged results to merged_docking_results.csv (total rows: {len(final_df)})")
- else:
- print("\n❌ No valid results found.")
- if __name__ == "__main__":
- main()
- final_df = pd.read_csv('data/merged_docking_results1.csv')
- final_df['ligand'] = final_df.file.str[:-8].astype('int')
- final_df = final_df[final_df['ligand']<30]
- final_df[['energy', 'protein', 'ligand']].to_csv('data/3_docking_results.csv',index=False)
Receptor Preparation and Structure-based Screeening.ipynb at commit a53cfe6, no license · at the source
Overview
- State Key Laboratory of Mechanism and Quality of Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Bioengineering Department and Imperial-X, Imperial College London, London W12 7SL, United Kingdom
- Guangdong Engineering Technology Research Center of Biological Targeting Diagnosis, Therapy and Rehabilitation, The Fifth Affiliated Hospital, Guangzhou Medical University, No.621 Gangwan Road, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog 1478, Norway
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
- Cardiovascular Research Centre, Royal Brompton Hospital, London SW3 6NP, United Kingdom
- School of Biomedical Engineering & Imaging Sciences, King's College London, London WC2R 2LS, United Kingdom
- The Norwegian Centre on Healthy Ageing (NO-Age) and the Norwegian National anti-Alzheimer’s Disease (NO-AD) Networks, Oslo, Norway
Abstract
Lysosomal dysfunction is a core pathological driver of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Transcription factor EB (TFEB) serves as a master regulator of lysosomal biogenesis, and its pharmacological activation represents a strategy to restore lysosomal function in disease and aging. Here, using a series of artificial intelligence-powered computational virtual screening workflows, we have identified isoginkgetin (ISO), a small-molecule compound, as a potent TFEB activator that promotes mechanistic target of rapamycin complex 1 (mTORC1)–independent TFEB nuclear translocation to enhance lysosomal biogenesis and function. Mechanistically, ISO functions as an ATP-competitive inhibitor that binds to the key Lys85 residue within the ATP-binding pocket of glycogen synthase kinase 3β (GSK-3β), thereby regulating the GSK-3β–TFEB signaling axis to activate TFEB nuclear translocation. Functionally, ISO improves lysosomal function and protects motor neurons differentiated from induced pluripotent stem cells derived from patients with ALS from degeneration. Collectively, these results support the hypothesis that lysosomal dysfunction is a druggable target for ALS.
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 1 match between paragraphs and lines of code.
XiangLuXiao/mTORIndependentCompoundScreen
a53cfe601a83501e47ff804dd49c62cf1fd51215, 20 January 2026Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
3 files
- Post-Docking Analysis.ipynb, Jupyter, 38 lines
- Receptor Preparation and Structure-based Screeening.ipynb, Jupyter, 493 lines, 1 match
- readme.md, Text, 53 lines
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;
- 2 scripts, each with its path and the digest of its content;
- 1 match 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
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Data availability
Data will be made available on request.
All raw data for the paper can be downloaded via the WeTransfer link.all the original data (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, 30 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 14 authors, 5 keywords, 11 MeSH terms, 26 funders, 67 references.
Cite
This paper
Li, A., Xiao, X., Liu, G., Li, K., Ling, Y., Deng, S., Xu, C., Cao, S.-Q., Wen, J., Lu, G., Yang, G., Fang, E. F., Qin, D., & Su, H. (2026). Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis. Pharmacological research, 227, 108172. https://
BibTeX
@article{li2026isoginkge
author = {Li, Ang and Xiao, Xianglu and Liu, Guopan and Li, Krinos and Ling, Yixia and Deng, Shenglong and Xu, Chunzuan and Cao, Shu-Qin and Wen, Jing and Lu, Guang and Yang, Guang and Fang, Evandro F. and Qin, Dajiang and Su, Huanxing},
title = {{Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis}},
journal = {Pharmacological research},
year = {2026},
month = mar,
volume = {227},
pages = {108172},
publisher = {Elsevier BV},
issn = {1043-6618},
doi = {10.1016/
url = {https://
pmid = {41912102},
pmcid = {PMC13132972}
}
RIS
TY - JOUR
AU - Li, Ang
AU - Xiao, Xianglu
AU - Liu, Guopan
AU - Li, Krinos
AU - Ling, Yixia
AU - Deng, Shenglong
AU - Xu, Chunzuan
AU - Cao, Shu-Qin
AU - Wen, Jing
AU - Lu, Guang
AU - Yang, Guang
AU - Fang, Evandro F.
AU - Qin, Dajiang
AU - Su, Huanxing
TI - Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis
T2 - Pharmacological research
J2 - Pharmacol Res
PY - 2026
DA - 2026/
VL - 227
SP - 108172
SN - 1043-6618
PB - Elsevier BV
DO - 10.1016/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1016/
"type": "article-journal",
"title": "Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis",
"container-title": "Pharmacological research",
"author": [
{
"family": "Li",
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"family": "Xiao",
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{
"family": "Liu",
"given": "Guopan"
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{
"family": "Li",
"given": "Krinos"
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{
"family": "Ling",
"given": "Yixia"
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{
"family": "Deng",
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{
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{
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"given": "Guang"
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{
"family": "Yang",
"given": "Guang"
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{
"family": "Fang",
"given": "Evandro F."
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{
"family": "Qin",
"given": "Dajiang"
},
{
"family": "Su",
"given": "Huanxing"
}
],
"container-title-short":
"volume": "227",
"page": "108172",
"DOI": "10.1016/
"PMID": "41912102",
"PMCID": "PMC13132972",
"ISSN": "1043-6618",
"publisher": "Elsevier BV",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
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28
]
]
}
}
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