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  1. Article ; Online: Classifying Future Healthcare Utilization in COPD Using Quantitative CT Lung Imaging and Two-Step Feature Selection via Sparse Subspace Learning with the CanCOLD Study.

    Moslemi, Amir / Hague, Cameron J / Hogg, James C / Bourbeau, Jean / Tan, Wan C / Kirby, Miranda

    Academic radiology

    2024  

    Abstract: Rationale: Although numerous candidate features exist for predicting risk of higher risk of healthcare utilization in patients with chronic obstructive pulmonary disease (COPD), the process for selecting the most discriminative features remains unclear.! ...

    Abstract Rationale: Although numerous candidate features exist for predicting risk of higher risk of healthcare utilization in patients with chronic obstructive pulmonary disease (COPD), the process for selecting the most discriminative features remains unclear.
    Objective: The objective of this study was to develop a robust feature selection method to identify the most discriminative candidate features for predicting healthcare utilization in COPD, and compare the model performance with other common feature selection methods.
    Materials and methods: In this retrospective study, demographic, lung function measurements and CT images were collected from 454 COPD participants from the Canadian Cohort Obstructive Lung Disease study from 2010-2017. A follow-up visit was completed approximately 1.5 years later and participants reported healthcare utilization. CT analysis was performed for feature extraction. A two-step hybrid feature selection method was proposed that utilized: (1) sparse subspace learning with nonnegative matrix factorization, and, (2) genetic algorithm. Seven commonly used feature selection methods were also implemented that reported the top 10 or 20 features for comparison. Performance was evaluated using accuracy.
    Results: Of the 454 COPD participants evaluated, 161 (35%) utilized healthcare services at follow-up. The accuracy for predicting subsequent healthcare utilization for the seven commonly used feature selection methods ranged from 72%-76% with the top 10 features, and 77%-80% with the top 20 features. Relative to these methods, hybrid feature selection obtained significantly higher accuracy for predicting subsequent healthcare utilization at 82% ± 3% (p < 0.05). Selected features with the proposed method included: DL
    Conclusion: The hybrid feature selection method identified the most discriminative features for classifying individuals with and without future healthcare utilization, and increased the accuracy compared to other state-of-the-art approaches.
    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1355509-1
    ISSN 1878-4046 ; 1076-6332
    ISSN (online) 1878-4046
    ISSN 1076-6332
    DOI 10.1016/j.acra.2024.03.030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Update on the Pathogenesis of COPD. Reply.

    Agustí, Alvar / Hogg, James C

    The New England journal of medicine

    2019  Volume 381, Issue 25, Page(s) 2484

    MeSH term(s) Humans ; Pulmonary Disease, Chronic Obstructive
    Language English
    Publishing date 2019-12-20
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc1914437
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: CT Imaging With Machine Learning for Predicting Progression to COPD in Individuals at Risk.

    Makimoto, Kalysta / Hogg, James C / Bourbeau, Jean / Tan, Wan C / Kirby, Miranda

    Chest

    2023  Volume 164, Issue 5, Page(s) 1139–1149

    Abstract: Background: Identifying individuals at risk of progressing to COPD may allow for initiation of treatment to potentially slow the progression of the disease or the selection of subgroups for discovery of novel interventions.: Research question: Does ... ...

    Abstract Background: Identifying individuals at risk of progressing to COPD may allow for initiation of treatment to potentially slow the progression of the disease or the selection of subgroups for discovery of novel interventions.
    Research question: Does the addition of CT imaging features, texture-based radiomic features, and established quantitative CT scan to conventional risk factors improve the performance for predicting progression to COPD in individuals who smoke with machine learning?
    Study design and methods: Participants at risk (individuals who currently or formerly smoked, without COPD) from the Canadian Cohort Obstructive Lung Disease (CanCOLD) population-based study underwent CT imaging at baseline and spirometry at baseline and follow-up. Various combinations of CT scan features, texture-based CT scan radiomics (n = 95), and established quantitative CT scan (n = 8), as well as demographic (n = 5) and spirometry (n = 3) measurements, with machine learning algorithms were evaluated to predict progression to COPD. Performance metrics included the area under the receiver operating characteristic curve (AUC) to evaluate the models. DeLong test was used to compare the performance of the models.
    Results: Among the 294 at-risk participants who were evaluated (mean age, 65.6 ± 9.2 years; 42% female; mean pack-years, 17.9 ± 18.7), 52 participants (23.7%) in the training data set and 17 participants (23.0%) in the testing data set progressed to spirometric COPD at follow-up (2.5 ± 0.9 years from baseline). Compared with machine learning models with demographics alone (AUC, 0.649), the addition of CT imaging features to demographics (AUC, 0.730; P < .05) or CT imaging features and spirometry to demographics (AUC, 0.877; P < .05) significantly improved the performance for predicting progression to COPD.
    Interpretation: Heterogeneous structural changes occur in the lungs of individuals at risk that can be quantified using CT imaging features, and evaluation of these features together with conventional risk factors improves performance for predicting progression to COPD.
    MeSH term(s) Humans ; Female ; Middle Aged ; Aged ; Male ; Canada/epidemiology ; Lung/diagnostic imaging ; Tomography, X-Ray Computed/methods ; Machine Learning ; Pulmonary Disease, Chronic Obstructive/diagnostic imaging
    Language English
    Publishing date 2023-06-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1032552-9
    ISSN 1931-3543 ; 0012-3692
    ISSN (online) 1931-3543
    ISSN 0012-3692
    DOI 10.1016/j.chest.2023.06.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Update on the Pathogenesis of Chronic Obstructive Pulmonary Disease.

    Agustí, Alvar / Hogg, James C

    The New England journal of medicine

    2019  Volume 381, Issue 13, Page(s) 1248–1256

    MeSH term(s) Disease Progression ; Gene-Environment Interaction ; Humans ; Lung/growth & development ; Lung/physiology ; Pulmonary Disease, Chronic Obstructive/etiology ; Pulmonary Disease, Chronic Obstructive/genetics ; Risk Factors ; Smoking/adverse effects
    Language English
    Publishing date 2019-10-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMra1900475
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Intratumoral T-cell receptor repertoire composition predicts overall survival in patients with pancreatic ductal adenocarcinoma.

    Pothuri, Vikram S / Hogg, Graham D / Conant, Leah / Borcherding, Nicholas / James, C Alston / Mudd, Jacqueline / Williams, Greg / Seo, Yongwoo David / Hawkins, William G / Pillarisetty, Venu G / DeNardo, David G / Fields, Ryan C

    Oncoimmunology

    2024  Volume 13, Issue 1, Page(s) 2320411

    Abstract: Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is refractory to immune checkpoint inhibitor therapy. However, intratumoral T-cell infiltration correlates with improved overall survival (OS). Herein, we characterized the diversity and ...

    Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is refractory to immune checkpoint inhibitor therapy. However, intratumoral T-cell infiltration correlates with improved overall survival (OS). Herein, we characterized the diversity and antigen specificity of the PDAC T-cell receptor (TCR) repertoire to identify novel immune-relevant biomarkers. Demographic, clinical, and TCR-beta sequencing data were collated from 353 patients across three cohorts that underwent surgical resection for PDAC. TCR diversity was calculated using Shannon Wiener index, Inverse Simpson index, and "True entropy." Patients were clustered by shared repertoire specificity. TCRs predictive of OS were identified and their associated transcriptional states were characterized by single-cell RNAseq. In multivariate Cox regression models controlling for relevant covariates, high intratumoral TCR diversity predicted OS across multiple cohorts. Conversely, in peripheral blood, high abundance of T-cells, but not high diversity, predicted OS. Clustering patients based on TCR specificity revealed a subset of TCRs that predicts OS. Interestingly, these TCR sequences were more likely to encode CD8
    MeSH term(s) Humans ; Pancreatic Neoplasms/diagnosis ; Pancreatic Neoplasms/genetics ; Carcinoma, Pancreatic Ductal/diagnosis ; Carcinoma, Pancreatic Ductal/genetics ; T-Lymphocytes ; Receptors, Antigen, T-Cell/genetics ; Biomarkers
    Chemical Substances Receptors, Antigen, T-Cell ; Biomarkers
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2645309-5
    ISSN 2162-402X ; 2162-402X
    ISSN (online) 2162-402X
    ISSN 2162-402X
    DOI 10.1080/2162402X.2024.2320411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Reply to Cottin: Small Airways in Pulmonary Fibrosis: Revisiting an Old Question with New Tools.

    Vasilescu, Dragoş M / Ikezoe, Kohei / Ryerson, Christopher J / Hogg, James C / Hackett, Tillie-Louise

    American journal of respiratory and critical care medicine

    2022  Volume 206, Issue 4, Page(s) 517

    MeSH term(s) Cystic Fibrosis/pathology ; Humans ; Lung/diagnostic imaging ; Lung/pathology ; Pulmonary Fibrosis/complications ; Pulmonary Fibrosis/pathology
    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202203-0502LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Structure and Function Relationships in Diseases of the Small Airways.

    Hogg, James C / Hackett, Tillie-Louise

    Annals of the American Thoracic Society

    2018  Volume 15, Issue Suppl 1, Page(s) S18–S25

    Abstract: It is well known that particulate matter suspended in the earth's atmosphere generated by tobacco smoke, automobile exhaust, industrial processes, and forest fires has been identified as a major risk factor for chronic lung disease. Particulate matter ... ...

    Abstract It is well known that particulate matter suspended in the earth's atmosphere generated by tobacco smoke, automobile exhaust, industrial processes, and forest fires has been identified as a major risk factor for chronic lung disease. Particulate matter can be divided into large, intermediate, and fine particulates. When inhaled, large particulates develop sufficient momentum to leave the flowing stream of inhaled air and deposit by impaction in the nose, mouth, nasopharynx, larynx, trachea, and central bronchi. Intermediate-sized particulates that develop less momentum deposit in the smaller bronchi and larger bronchioles, and the finest particulates that develop the least momentum make it to the distal gas-exchanging tissue, where gas moves solely by diffusion. On the basis of Einstein's classic work on Brownian motion that showed particles suspended in a gas diffuse much more slowly than the gas in which they are suspended, we postulate that the small airways that accommodate the shift from bulk airflow to diffusion become the major site for deposition of fine particles, resulting in a host immune response. Much remains to be learned about the interaction between the deposition of fine particulates and the host immune and tissue responses; the purpose of this review is to examine the hypothesis that the smallest conducting airways and proximal gas-exchanging tissue are the primary sites for the deposition of the finest particulates inhaled into the lungs.
    MeSH term(s) Airway Remodeling ; Disease Susceptibility ; Humans ; Inhalation Exposure/adverse effects ; Lung/pathology ; Particulate Matter/analysis ; Pulmonary Disease, Chronic Obstructive/etiology ; Pulmonary Disease, Chronic Obstructive/physiopathology
    Chemical Substances Particulate Matter
    Language English
    Publishing date 2018-02-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2717461-X
    ISSN 2325-6621 ; 1943-5665 ; 2325-6621
    ISSN (online) 2325-6621 ; 1943-5665
    ISSN 2325-6621
    DOI 10.1513/AnnalsATS.201710-809KV
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Mian: interactive web-based microbiome data table visualization and machine learning platform.

    Jin, Boyang Tom / Xu, Feng / Ng, Raymond T / Hogg, James C

    Bioinformatics (Oxford, England)

    2021  Volume 38, Issue 4, Page(s) 1176–1178

    Abstract: Summary: Mian is a web application to interactively visualize, run statistical tools and train machine learning models on operational taxonomic unit (OTU) or amplicon sequence variant (ASV) datasets to identify key taxonomic groups, diversity trends or ... ...

    Abstract Summary: Mian is a web application to interactively visualize, run statistical tools and train machine learning models on operational taxonomic unit (OTU) or amplicon sequence variant (ASV) datasets to identify key taxonomic groups, diversity trends or taxonomic composition shifts in the context of provided categorical or numerical sample metadata. Tools, including Fisher's exact test, Boruta feature selection, alpha and beta diversity, and random forest and deep neural network classifiers, facilitate open-ended data exploration and hypothesis generation on microbial datasets.
    Availability: Mian is freely available at: miandata.org. Mian is an open-source platform licensed under the MIT license with source code available at github.com/tbj128/mian.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Microbiota ; Data Visualization ; Machine Learning ; Internet
    Language English
    Publishing date 2021-11-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab754
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A pathologist's view of airway obstruction in chronic obstructive pulmonary disease.

    Hogg, James C

    American journal of respiratory and critical care medicine

    2012  Volume 186, Issue 5, Page(s) v–vii

    MeSH term(s) Bronchioles/pathology ; Bronchography ; Humans ; Multidetector Computed Tomography ; Pulmonary Disease, Chronic Obstructive/diagnostic imaging ; Pulmonary Disease, Chronic Obstructive/pathology
    Language English
    Publishing date 2012-08-31
    Publishing country United States
    Document type Editorial
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201206-1130ED
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A brief review of chronic obstructive pulmonary disease.

    Hogg, James C

    Canadian respiratory journal

    2012  Volume 19, Issue 6, Page(s) 381–384

    Abstract: A recent study, based on a combination of multidetector computed tomography scanning of an intact specimen with microcomputed tomography and histological analysis of lung tissue samples, reported that the number of terminal bronchioles were reduced from ... ...

    Abstract A recent study, based on a combination of multidetector computed tomography scanning of an intact specimen with microcomputed tomography and histological analysis of lung tissue samples, reported that the number of terminal bronchioles were reduced from approximately 44,500/lung pair in control (donor) lungs to approximately 4800/lung pair in lungs donated by individuals with very severe (Global initiative for chronic Obstructive Lung Disease stage 4) chronic obstructive pulmonary disease (COPD) treated by lung transplantation. The present short review discusses the hypothesis that a rapid rate of terminal bronchiolar destruction causes the rapid decline in lung function leading to advanced COPD. With respect to why the terminal bronchioles are targeted for destruction, the postulated mechanisms of this destruction and the possibility that new treatments are able to either prevent or reverse the underlying cause of airway obstruction in COPD are addressed.
    MeSH term(s) Bronchioles/pathology ; Bronchioles/physiopathology ; Humans ; Multidetector Computed Tomography ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Pulmonary Disease, Chronic Obstructive/etiology ; Pulmonary Disease, Chronic Obstructive/therapy
    Language English
    Publishing date 2012-11-13
    Publishing country Egypt
    Document type Journal Article ; Review
    ZDB-ID 1213103-9
    ISSN 1916-7245 ; 1198-2241
    ISSN (online) 1916-7245
    ISSN 1198-2241
    DOI 10.1155/2012/496563
    Database MEDical Literature Analysis and Retrieval System OnLINE

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