Datasets:
pmc_id stringlengths 8 11 | title stringlengths 0 624 | abstract stringlengths 0 7.73k | main_text stringlengths 0 8.7M | authors listlengths 0 100 | journal stringlengths 3 168 | doi stringlengths 0 47 | pmid stringlengths 0 8 | publish_date stringclasses 1
value | stxbp1_mentions int64 0 0 | munc18_mentions int64 0 0 | num_figures int64 0 1.11k | num_images int64 0 1.11k | abstract_length int64 0 7.73k | main_text_length int64 0 8.7M |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PMC10000387 | Implementation of Exome Sequencing in Prenatal Diagnostics: Chances and Challenges | Whole exome sequencing (WES) has become part of the postnatal diagnostic work-up of both pediatric and adult patients with a range of disorders. In the last years, WES is slowly being implemented in the prenatal setting as well, although some hurdles remain, such as quantity and quality of input material, minimizing tu... | ## 1. Introduction
Major congenital anomalies (MCA) have a prevalence of 2β3% and are responsible for a significant percentage of pre- and perinatal demise and neonatal morbidity [1,2]. The etiology is heterogeneous, ranging from prenatal infections over teratologic agents to genetic causes.
Chromosomal microarray an... | [
"Ewa Janicki",
"Marjan De Rademaeker",
"Colombine Meunier",
"Nele Boeckx",
"Bettina Blaumeiser",
"Katrien Janssens"
] | Diagnostics | 10.3390/diagnostics13050860 | 36900003 | 0 | 0 | 4 | 4 | 1,310 | 26,018 | |
PMC10001118 | Epigenetics in LMNA-Related Cardiomyopathy | Mutations in the gene for lamin A/C(LMNA)cause a diverse range of diseases known as laminopathies.LMNA-related cardiomyopathy is a common inherited heart disease and is highly penetrant with a poor prognosis. In the past years, numerous investigations using mouse models, stem cell technologies, and patient samples have... | ## 1. Introduction
Mutations in genes encoding proteins of the nuclear lamina result in wide-ranging clinical phenotypes collectively referred to as laminopathies [1]. Many of these diseases are caused by mutations in the gene for lamin A/C (LMNA) and affect primarily the muscles, the peripheral nerves, and the adipos... | [
"Yinuo Wang",
"Gergana Dobreva"
] | Cells | 10.3390/cells12050783 | 36899919 | 0 | 0 | 3 | 3 | 948 | 37,302 | |
PMC10002385 | Application of Nicotinamide to Culture Medium Improves the Efficiency of Genome Editing in Hexaploid Wheat | Histone acetylation is the earliest and most well-characterized of post-translation modifications. It is mediated by histone acetyltransferases (HAT) and histone deacetylases (HDAC). Histone acetylation could change the chromatin structure and status and further regulate gene transcription. In this study, nicotinamide,... | ## 1. Introduction
The development and application of genome editing technology has provided important technical support for plant functional gene research and crop genetic improvement. Compared with other developed genome editing technologies, CRISPR/Cas systems have the advantages of simple operation and high effici... | [
"Wanxin Wang",
"Peipei Huang",
"Wenshuang Dai",
"Huali Tang",
"Yuliang Qiu",
"Yanan Chang",
"Zhiyang Han",
"Xi Li",
"Lipu Du",
"Xingguo Ye",
"Cheng Zou",
"Ke Wang"
] | International Journal of Molecular Sciences | 10.3390/ijms24054416 | 36901844 | 0 | 0 | 5 | 5 | 1,855 | 28,754 | |
PMC10002423 | Unveil the Secret of the Bacteria and Phage Arms Race | Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phageβs nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and ot... | ## 1. Introduction
Bacteria and bacteriophages (phages for short) have been engaged in a constant and repeated arms race and have coexisted steadily for billions of years. Phages outnumber bacteria by ten to one and are widely recognized as the most diverse of microbes. Phages can be divided into temperate phages and ... | [
"Yuer Wang",
"Huahao Fan",
"Yigang Tong"
] | International Journal of Molecular Sciences | 10.3390/ijms24054363 | 36901793 | 0 | 0 | 7 | 7 | 1,562 | 50,162 | |
PMC10002487 | Why Donβt the Mutant Cells That Evade DNA Repair Cause Cancer More Frequently? Importance of the Innate Immune System in the Tumor Microenvironment | The standard of care for most malignant solid tumors still involves tumor resection followed by chemo- and radiation therapy, hoping to eliminate the residual tumor cells. This strategy has been successful in extending the life of many cancer patients. Still, for primary glioblastoma (GBM), it has not controlled recurr... | ## 1. Introduction
Glioblastoma (GBM) is one of the deadliest forms of cancer, with an average life expectancy of about 14β18 months from detection [1]. The standard of care (SOC) for GBM is surgical resection of the tumor followed by chemo and or radiation therapy to eliminate the residual cancer cells [2,3]. However... | [
"Shubhasmita Mohapatra",
"Jared Cafiero",
"Khosrow Kashfi",
"Parag Mehta",
"Probal Banerjee"
] | International Journal of Molecular Sciences | 10.3390/ijms24055026 | 36902456 | 0 | 0 | 2 | 2 | 1,808 | 40,746 | |
PMC10002506 | Plant Protection against Viruses: An Integrated Review of Plant Immunity Agents | "Plant viruses are an important class of pathogens that seriously affect plant growth and harm crop (...TRUNCATED) | "## 1. Introduction\n\nCurrently, most conventional pesticides are expected to comprehensively preve(...TRUNCATED) | [
"Min Huang",
"Zilin Wu",
"Jingxin Li",
"Yuyu Ding",
"Shilin Chen",
"Xiangyang Li"
] | International Journal of Molecular Sciences | 10.3390/ijms24054453 | 36901884 | 0 | 0 | 3 | 3 | 1,081 | 26,133 | |
PMC10002644 | Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor | "Assays detecting viral infections play a significant role in limiting the spread of diseases such a(...TRUNCATED) | "## Design principles of Rolosense platform\n\nWe first functionalized DNA-based motors and chips wi(...TRUNCATED) | ["Selma Piranej","Luona Zhang","Alisina Bazrafshan","Mariana Marin","Gregory B Melikyan","Khalid Sal(...TRUNCATED) | bioRxiv | 10.1101/2023.02.27.530294 | 36909543 | 0 | 0 | 6 | 6 | 1,186 | 41,272 | |
PMC10003097 | New advances in CRISPR/Cas-mediated precise gene-editing techniques | "Over the past decade, CRISPR/Cas-based gene editing has become a powerful tool for generating mutat(...TRUNCATED) | "## Introduction\n\nGene editing via CRISPR/Cas technology has become a key tool for researchers in (...TRUNCATED) | [
"Chris Richardson",
"Robert N Kelsh",
"Rebecca J Richardson"
] | Disease Models & Mechanisms | 10.1242/dmm.049874 | 36847161 | 0 | 0 | 3 | 3 | 1,301 | 46,714 | |
PMC10003248 | The Landscape of Circular RNAs in Cardiovascular Diseases | "Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRN(...TRUNCATED) | "## 1. Introduction\n\nThe incidence of cardiovascular disease (CVD) has been increasing rapidly in (...TRUNCATED) | [
"Qi Long",
"Bingjie Lv",
"Shijiu Jiang",
"Jibin Lin"
] | International Journal of Molecular Sciences | 10.3390/ijms24054571 | 36902000 | 0 | 0 | 2 | 2 | 557 | 33,996 | |
PMC10003267 | "Engineering of DNA Structures Attached to Magnetic Particles for Effective Trans- and Cis-Cleavage (...TRUNCATED) | "Sequence-specific endonuclease Cas12-based biosensors have rapidly evolved as a strong tool to dete(...TRUNCATED) | "## 1. Introduction\n\nCRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISP(...TRUNCATED) | [
"Aleksandr V Ivanov",
"Irina V Safenkova",
"Sergey F Biketov",
"Anatoly V Zherdev",
"Boris B Dzantiev"
] | International Journal of Molecular Sciences | 10.3390/ijms24054484 | 36901914 | 0 | 0 | 5 | 5 | 1,518 | 39,207 |
End of preview. Expand in Data Studio
source_datasets: - PubMed Central
STXBP1 PubMed Central Full-Text Dataset v2
A comprehensive collection of 31,786 full-text scientific articles from PubMed Central related to STXBP1, synaptic function, and neurological research.
π Version 2 Updates (December 2025)
- Complete re-extraction with improved HTML parsing
- Full main text with proper section headers
- Enhanced metadata extraction
- 99.7% figure-image matching (see companion multimodal dataset)
Dataset Overview
| Metric | Value |
|---|---|
| Total Articles | 31,786 |
| Articles with STXBP1 mentions | 1,335 |
| Articles with Munc18 mentions | 1,200+ |
| Articles with abstract: 30,856 | |
| Total Abstract Characters | ~45 million |
| Articles with main_text: 31,684 | |
| Total Main Text Characters | ~1.44 billion |
| Average Abstract Length | 1,421 chars |
| Average Main Text Length | 45,391 chars |
Schema
| Column | Type | Description |
|---|---|---|
pmc_id |
string | PubMed Central ID (e.g., "PMC10196665") |
title |
string | Article title |
abstract |
string | Article abstract |
main_text |
string | Full article text with section headers |
authors |
string | Author list |
journal |
string | Journal name |
doi |
string | Digital Object Identifier |
pmid |
string | PubMed ID |
publish_date |
string | Publication date |
stxbp1_mentions |
int | Count of STXBP1 mentions in text |
munc18_mentions |
int | Count of Munc18 mentions in text |
num_figures |
int | Number of figures in article |
num_images |
int | Number of matched figure images |
abstract_length |
int | Character count of abstract |
main_text_length |
int | Character count of main text |
Usage
Load with Hugging Face Datasets
from datasets import load_dataset
dataset = load_dataset("SkyWhal3/stxbp1-pubmed-central-fulltext")
# Access the data
df = dataset['train'].to_pandas()
# Filter STXBP1-specific articles
stxbp1_articles = df[df['stxbp1_mentions'] > 0]
print(f"Found {len(stxbp1_articles)} STXBP1-related articles")
Load with Pandas
import pandas as pd
df = pd.read_parquet("hf://datasets/SkyWhal3/stxbp1-pubmed-central-fulltext/stxbp1_pubmed_articles.parquet")
Example Queries
# Find articles about specific topics
seizure_articles = df[df['main_text'].str.contains('seizure', case=False, na=False)]
# Get articles with most STXBP1 mentions
top_stxbp1 = df.nlargest(10, 'stxbp1_mentions')[['pmc_id', 'title', 'stxbp1_mentions']]
# Find articles by keyword in title
crispr_articles = df[df['title'].str.contains('CRISPR|gene therapy', case=False, na=False)]
Related Resources
| Resource | Description | Link |
|---|---|---|
| Multimodal Dataset | Same articles + 170K figure images | SkyWhal3/STXBP1_PubMed_Central_Multimodal_Dataset |
| ClinVar Dataset | STXBP1 genetic variants | SkyWhal3/stxbp1-clinvar |
| Trained Model | Fine-tuned Qwen3-VL-8B | Coming soon! |
About STXBP1
STXBP1 (Syntaxin-Binding Protein 1), also known as Munc18-1, is essential for synaptic vesicle fusion and neurotransmitter release. Mutations cause STXBP1 Encephalopathy, a rare neurological disorder characterized by:
- Early-onset epilepsy
- Developmental delays
- Movement disorders
- Intellectual disability
This dataset supports AI-powered research into understanding and treating STXBP1-related conditions.
Citation
@dataset{stxbp1_fulltext_2025,
author = {SkyWhal3},
title = {STXBP1 PubMed Central Full-Text Dataset},
year = {2025},
publisher = {Hugging Face},
url = {https://huggingface.co/datasets/SkyWhal3/stxbp1-pubmed-central-fulltext}
}
License
CC-BY-4.0. Source articles are from PubMed Central's Open Access subset.
Changelog
v2.0 (December 2025)
- Complete re-extraction with improved parsing
- Added section headers to main_text
- Enhanced metadata fields
- Added figure/image counts
- Added text length statistics
v1.0 (December 2025)
- Initial release
This dataset is dedicated to all children and families affected by STXBP1 Encephalopathy.
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