Evidence map›Paper›PMID 38651949›Full record

ArticleAmerican journal of physiology. Gastrointestinal and liver physiology2024

BiliQML: a supervised machine-learning model to quantify biliary forms from digitized whole slide liver histopathological images.

Dominick J Hellen, Meredith E Fay, David H Lee, Caroline Klindt-Morgan, Ashley Bennett, Kimberly J Pachura, Arash Grakoui, Stacey S Huppert, Paul A Dawson, Wilbur A Lam and 1 more

Open access · greenAbstract read
In one paragraph

Article in American journal of physiology. Gastrointestinal and liver physiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
1.1field-weighted citation impact, top 20% of its field
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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Review
  2. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 3 institutions in 1 country.

Dominick J HellenDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.ORCID 0000-0002-2793-399X
Meredith E FayThe Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States.
David H LeeDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.
Caroline Klindt-MorganDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.
Ashley BennettDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.
Kimberly J PachuraDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.
Arash GrakouiEmory National Primate Research Center, Division of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States.
Stacey S HuppertDivision of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States.
Paul A DawsonDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.ORCID 0000-0001-9760-4422
Wilbur A LamThe Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States.
Saul J KarpenDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia, United States.ORCID 0000-0002-3379-7592
Emory University · USGeorgia Institute of Technology · USCincinnati Children's Hospital Medical Center · US

Funding

Technology Training and Dissemination CoreU54EB027690 · NIBIB · EMORY UNIVERSITY · PI Wilbur A Lam · 2018 to 2026
$96.1M
Protective immunity to HCV and rational vaccine designU19AI159819 · NIAID · EMORY UNIVERSITY · PI Arash Grakoui · 2021 to 2026
$16.6M
TRAINING GRANTS IN ENVIROMENTAL TOXICOLOGYT32ES007020 · NIEHS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI ESSIGMANN, JOHN M · 1985 to 2024
$13.1M
PREDOCTORAL TRAINING PROGRAM IN GENETICST32GM008490 · NIGMS · EMORY UNIVERSITY · PI BOSS, JEREMY M. · 1993 to 2022
$8.0M
ILEAL BILE ACID TRANSPORTER METABOLISM AND REGULATIONR01DK047987 · NIDDK · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI DAWSON, PAUL A · 2000 to 2021
$6.8M
Engineering biophysical microtechnologies for hematologic applications in health and diseaseR35HL145000 · NHLBI · EMORY UNIVERSITY · PI LAM, WILBUR A · 2019 to 2025
$5.0M
Dynamics of antigen specific B and Tfh responses during acute and chronic HCVR01AI136533 · NIAID · EMORY UNIVERSITY · PI GRAKOUI, ARASH · 2018 to 2022
$3.8M
T cell Immunity and the Outcome of Acute HCV InfectionR01AI126890 · NIAID · RESEARCH INST NATIONWIDE CHILDREN'S HOSP · PI GRAKOUI, ARASH, WALKER, CHRISTOPHER M. · 2016 to 2020
$3.7M
T cell compartmentalization and antiviral responseR01AI124680 · NIAID · EMORY UNIVERSITY · PI GRAKOUI, ARASH, ZHU, CHENG · 2016 to 2020
$3.2M
Modeling genetic contributions to biliary atresiaR01DK135815 · NIDDK · VIRGINIA COMMONWEALTH UNIVERSITY · PI SAUL J. KARPEN · 2023 to 2026
$2.4M
Molecular regulation of hepatic cell differentiation and maturationR01DK120765 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI HUPPERT, STACEY S · 2019 to 2022
$1.6M
Targeting POGLUT1 to promote biliary development in Alagille syndromeR01DK132751 · NIDDK · BAYLOR COLLEGE OF MEDICINE · PI HUPPERT, STACEY S, JAFAR-NEJAD, HAMED · 2022 to 2024
$1.2M
Chan Zuckerberg Initiative (CZI) PEDIATRIC LIVER CELL ATLASDeutsche Forschungsgemeinschaft (DFG) KL 3389/ 1-1 (707857/809459)HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI) R35HL145000HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI124680HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI126890HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) R01AI136533HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID) U19AI159819HHS | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB) U54 EB027690 02S1HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) F31DK137565HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) R01DK047987HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) R01DK120765HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) R01DK132751HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) R01DK135815HHS | NIH | National Institute of General Medical Sciences (NIGMS) 5T32GM008490-30NHLBI NIH HHS R35 HL145000NIAID NIH HHS R01 AI124680NIAID NIH HHS R01 AI126890NIAID NIH HHS R01 AI136533NIAID NIH HHS U19 AI159819NIBIB NIH HHS U54 EB027690NIDDK NIH HHS F31 DK137565NIDDK NIH HHS R01 DK047987NIDDK NIH HHS R01 DK120765NIDDK NIH HHS R01 DK132751NIDDK NIH HHS R01 DK135815NIEHS NIH HHS T32 ES007020NIGMS NIH HHS T32 GM008490
6 · The paper itself

Abstract

The progress of research focused on cholangiocytes and the biliary tree during development and following injury is hindered by limited available quantitative methodologies. Current techniques include two-dimensional standard histological cell-counting approaches, which are rapidly performed, error prone, and lack architectural context or three-dimensional analysis of the biliary tree in opacified livers, which introduce technical issues along with minimal quantitation. The present study aims to fill these quantitative gaps with a supervised machine-learning model (BiliQML) able to quantify biliary forms in the liver of anti-keratin 19 antibody-stained whole slide images. Training utilized 5,019 researcher-labeled biliary forms, which following feature selection, and algorithm optimization, generated an

Indexed as

LiverSupervised Machine LearningAnimalsBile Duct DiseasesBile DuctsBiliary TractDisease Models, AnimalImage Processing, Computer-AssistedMiceartificial intelligencecholangiocytecholangiopathyquantificationthree dimensional

Identifiers

PMID38651949
PMCPMC11376979
OpenAlexW4395037503

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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 Socratic graph.