Evidence map›Paper›PMID 39874947›Full record

ArticleCell reports methods2025

Analysis of TEM micrographs with deep learning reveals APOE genotype-specific associations between HDL particle diameter and Alzheimer's dementia.

Jack Jingyuan Zheng, Brian Vannak Hong, Joanne K Agus, Xinyu Tang, Fei Guo, Carlito B Lebrilla, Izumi Maezawa, Lee-Way Jin, Wyatt N Vreeland, Dean C Ripple and 1 more

Abstract read
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In one paragraph

Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Jack Jingyuan ZhengDepartment of Nutrition, University of California, Davis, Davis, CA 95616, USA.
Brian Vannak HongDepartment of Nutrition, University of California, Davis, Davis, CA 95616, USA.
Joanne K AgusDepartment of Nutrition, University of California, Davis, Davis, CA 95616, USA.
Xinyu TangDepartment of Nutrition, University of California, Davis, Davis, CA 95616, USA.
Fei GuoDepartment of Molecular and Cell Biology, University of California, Davis, Davis, CA 95616, USA.
Carlito B LebrillaDepartment of Chemistry, University of California, Davis, Davis, CA 95616, USA.
Izumi MaezawaDepartment of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA.
Lee-Way JinDepartment of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA.
Wyatt N VreelandBiomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Dean C RippleBiomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Angela M ZivkovicDepartment of Nutrition, University of California, Davis, Davis, CA 95616, USA. Electronic address: amzivkovic@ucdavis.edu.

Funding

UC Davis Alzheimer's Disease Research CenterP30AG072972 · NIA · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Charles DeCarli, Rachel A Whitmer · 2021 to 2026
$25.2M
Comprehensive Characterization of Glycosylation Alterations in Alzheimer’s DiseaseR01AG062240 · NIA · UNIVERSITY OF CALIFORNIA AT DAVIS · PI JIN, LEE-WAY, LEBRILLA, CARLITO B · 2018 to 2022
$3.3M
Development of a Novel Technology for Preparative Fractionation and Characterization of Lipoprotein ParticlesR01GM147545 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI ZIVKOVIC, ANGELA M · 2022 to 2025
$1.2M
Novel Separation Methods for exRNA Carriers: Extracellular Vesicles, Lipoprotein Particles, and Protein AggregatesUH3CA241694 · NCI · JOHNS HOPKINS UNIVERSITY · PI WITWER, KENNETH W · 2021 to 2022
$1.1M
Novel Separation Methods for exRNA Carriers: Extracellular Vesicles, Lipoprotein Particles, and Protein AggregatesUG3CA241694 · NCI · JOHNS HOPKINS UNIVERSITY · PI WITWER, KENNETH W · 2019 to 2020
$941k
NCI NIH HHS UG3 CA241694NCI NIH HHS UH3 CA241694NIA NIH HHS P30 AG072972NIA NIH HHS R01 AG062240NIGMS NIH HHS R01 GM147545
6 · The paper itself

Abstract

High-density lipoprotein (HDL) particle diameter distribution is informative in the diagnosis of many conditions, including Alzheimer's disease (AD). However, obtaining an accurate HDL size measurement is challenging. We demonstrated the utility of measuring the diameter of more than 1,800,000 HDL particles with the deep learning model YOLOv7 (you only look once) from micrographs of 183 HDL samples, including patients with dementia or normal cognition (controls). This method was shown to be more efficient and accurate than conventional image analysis software. Using this method, we found a higher abundance of small HDLs in participants with dementia compared to controls in patients with the apolipoprotein E (APOE) ε3ε4 genotype, whereas patients with the APOE ε3ε3 genotype had higher variability in the abundance of different HDL subclasses. Our results show an example of accurate individual HDL particle diameter measurement for large-scale clinical samples, which can be expanded to characterize the relationship between disease risk and other nanoparticles in the sub-20-nm diameter size range.

Indexed as

Alzheimer DiseaseApolipoproteins EDeep LearningLipoproteins, HDLAgedAged, 80 and overFemaleGenotypeHumansMaleParticle SizeApolipoproteins ELipoproteins, HDLagingAlzheimer’s diseasecomputer visionCP: Neurosciencedeep learningdementiaelectron microscopylipoproteinmetabolic diseaseneural networkobject detector

Identifiers

PMID39874947
PMCPMC11840948

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.