González G, Washko GR, San José Estépar R. Deep learning for biomarker regression: application to osteoporosis and emphysema on chest CT scans. Proc SPIE Int Soc Opt Eng 2018;10574Abstract
Introduction: Biomarker computation using deep-learning often relies on a two-step process, where the deep learning algorithm segments the region of interest and then the biomarker is measured. We propose an alternative paradigm, where the biomarker is estimated directly using a regression network. We showcase this image-to-biomarker paradigm using two biomarkers: the estimation of bone mineral density (BMD) and the estimation of lung percentage of emphysema from CT scans. Materials and methods: We use a large database of 9,925 CT scans to train, validate and test the network for which reference standard BMD and percentage emphysema have been already computed. First, the 3D dataset is reduced to a set of canonical 2D slices where the organ of interest is visible (either spine for BMD or lungs for emphysema). This data reduction is performed using an automatic object detector. Second, The regression neural network is composed of three convolutional layers, followed by a fully connected and an output layer. The network is optimized using a momentum optimizer with an exponential decay rate, using the root mean squared error as cost function. Results: The Pearson correlation coefficients obtained against the reference standards are = 0.940 ( < 0.00001) and = 0.976 ( < 0.00001) for BMD and percentage emphysema respectively. Conclusions: The deep-learning regression architecture can learn biomarkers from images directly, without indicating the structures of interest. This approach simplifies the development of biomarker extraction algorithms. The proposed data reduction based on object detectors conveys enough information to compute the biomarkers of interest.
Reyfman PA, Washko GR, Dransfield MT, Spira A, Han MLK, Kalhan R. Defining Impaired Respiratory Health. A Paradigm Shift for Pulmonary Medicine. Am J Respir Crit Care Med 2018;198(4):440-446.
Diaz AA, Strand M, Coxson HO, Ross JC, Estepar RSJ, Lynch D, van Rikxoort EM, Rosas IO, Hunninghake GM, Putman RK, Hatabu H, Yen A, Kinney GL, Hokanson JE, Silverman EK, Crapo J, Washko GR. Disease Severity Dependence of the Longitudinal Association Between CT Lung Density and Lung Function in Smokers. Chest 2018;153(3):638-645.Abstract
BACKGROUND: In smokers, the lung parenchyma is characterized by inflammation and emphysema, processes that can result in local gain and loss of lung tissue. CT measures of lung density might reflect lung tissue changes; however, longitudinal data regarding the effects of CT lung tissue on FEV in smokers with and without COPD are scarce. METHODS: The 15th percentile of CT lung density was obtained from the scans of 3,390 smokers who completed baseline and 5-year follow-up of the Genetic Epidemiology of COPD (COPDGene) study visits. The longitudinal relationship between total lung capacity-adjusted lung density (TLC-PD15) and FEV was assessed by using multivariable mixed models. Separate models were performed in smokers at risk, smokers with preserved ratio and impaired spirometry (PRISm), and smokers with COPD according to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) staging system. RESULTS: The direction of the relationship between lung density and lung function was GOLD stage dependent. In smokers with PRISm, a 1-g/L decrease in TLC-PD15 was associated with an increase of 2.8 mL FEV (P = .02). In contrast, among smokers with GOLD III to IV COPD, a 1-g/L decrease in TLC-PD15 was associated with a decrease of 4.1 mL FEV (P = .002). CONCLUSIONS: A decline in TLC-PD15 was associated with an increase or decrease in FEV depending on disease severity. The associations are GOLD stage specific, and their presence might influence the interpretation of future studies that use CT lung density as an intermediate study end point for a decline in lung function. TRIAL REGISTRY:; No.: NCT00608764; URL:
González G, Ash SY, Vegas-Sánchez-Ferrero G, Onieva Onieva J, Rahaghi FN, Ross JC, Díaz A, San José Estépar R, Washko GR. Disease Staging and Prognosis in Smokers Using Deep Learning in Chest Computed Tomography. Am J Respir Crit Care Med 2018;197(2):193-203.Abstract
RATIONALE: Deep learning is a powerful tool that may allow for improved outcome prediction. OBJECTIVES: To determine if deep learning, specifically convolutional neural network (CNN) analysis, could detect and stage chronic obstructive pulmonary disease (COPD) and predict acute respiratory disease (ARD) events and mortality in smokers. METHODS: A CNN was trained using computed tomography scans from 7,983 COPDGene participants and evaluated using 1,000 nonoverlapping COPDGene participants and 1,672 ECLIPSE participants. Logistic regression (C statistic and the Hosmer-Lemeshow test) was used to assess COPD diagnosis and ARD prediction. Cox regression (C index and the Greenwood-Nam-D'Agnostino test) was used to assess mortality. MEASUREMENTS AND MAIN RESULTS: In COPDGene, the C statistic for the detection of COPD was 0.856. A total of 51.1% of participants in COPDGene were accurately staged and 74.95% were within one stage. In ECLIPSE, 29.4% were accurately staged and 74.6% were within one stage. In COPDGene and ECLIPSE, the C statistics for ARD events were 0.64 and 0.55, respectively, and the Hosmer-Lemeshow P values were 0.502 and 0.380, respectively, suggesting no evidence of poor calibration. In COPDGene and ECLIPSE, CNN predicted mortality with fair discrimination (C indices, 0.72 and 0.60, respectively), and without evidence of poor calibration (Greenwood-Nam-D'Agnostino P values, 0.307 and 0.331, respectively). CONCLUSIONS: A deep-learning approach that uses only computed tomography imaging data can identify those smokers who have COPD and predict who are most likely to have ARD events and those with the highest mortality. At a population level CNN analysis may be a powerful tool for risk assessment.
Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018;12(1):1.Abstract
BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS: We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS: The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
Rice MB, Li W, Dorans KS, Wilker EH, Ljungman P, Gold DR, Schwartz J, Koutrakis P, Kloog I, Araki T, Hatabu H, Estepar RSJ, O'Connor GT, Mittleman MA, Washko GR. Exposure to Traffic Emissions and Fine Particulate Matter and Computed Tomography Measures of the Lung and Airways. Epidemiology 2018;29(3):333-341.Abstract
BACKGROUND: Exposure to ambient air pollution has been associated with lower lung function in adults, but few studies have investigated associations with radiographic lung and airway measures. METHODS: We ascertained lung volume, mass, density, visual emphysema, airway size, and airway wall area by computed tomography (CT) among 2,545 nonsmoking Framingham CT substudy participants. We examined associations of home distance to major road and PM2.5 (2008 average from a spatiotemporal model using satellite data) with these outcomes using linear and logistic regression models adjusted for age, sex, height, weight, census tract median household value and population density, education, pack-years of smoking, household tobacco exposure, cohort, and date. We tested for differential susceptibility by sex, smoking status (former vs. never), and cohort. RESULTS: The mean participant age was 60.1 years (standard deviation 11.9 years). Median PM2.5 level was 9.7 µg/m (interquartile range, 1.6). Living <100 m from a major road was associated with a 108 ml (95% CI = 8, 207) higher lung volume compared with ≥400 m away. There was also a log-linear association between proximity to road and higher lung volume. There were no convincing associations of proximity to major road or PM2.5 with the other pulmonary CT measures. In subgroup analyses, road proximity was associated with lower lung density among men and higher odds of emphysema among former smokers. CONCLUSIONS: Living near a major road was associated with higher average lung volume, but otherwise, we found no association between ambient pollution and radiographic measures of emphysema or airway disease.
Burkart KM, Sofer T, London SJ, Manichaikul A, Hartwig FP, Yan Q, Soler Artigas M, Avila L, Chen W, Davis Thomas S, Diaz AA, Hall IP, Horta BL, Kaplan RC, Laurie CC, Menezes AM, Morrison JV, Oelsner EC, Rastogi D, Rich SS, Soto-Quiros M, Stilp AM, Tobin MD, Wain LV, Celedón JC, Barr GR. A Genome-Wide Association Study in Hispanics/Latinos Identifies Novel Signals for Lung Function. The Hispanic Community Health Study/Study of Latinos. Am J Respir Crit Care Med 2018;198(2):208-219.Abstract
RATIONALE: Lung function and chronic obstructive pulmonary disease (COPD) are heritable traits. Genome-wide association studies (GWAS) have identified numerous pulmonary function and COPD loci, primarily in cohorts of European ancestry. OBJECTIVES: Perform a GWAS of COPD phenotypes in Hispanic/Latino populations to identify loci not previously detected in European populations. METHODS: GWAS of lung function and COPD in Hispanic/Latino participants from a population-based cohort. We performed replication studies of novel loci in independent studies. MEASUREMENTS AND MAIN RESULTS: Among 11,822 Hispanic/Latino participants, we identified eight novel signals; three replicated in independent populations of European Ancestry. A novel locus for FEV in ZSWIM7 (rs4791658; P = 4.99 × 10) replicated. A rare variant (minor allele frequency = 0.002) in HAL (rs145174011) was associated with FEV/FVC (P = 9.59 × 10) in a region previously identified for COPD-related phenotypes; it remained significant in conditional analyses but did not replicate. Admixture mapping identified a novel region, with a variant in AGMO (rs41331850), associated with Amerindian ancestry and FEV, which replicated. A novel locus for FEV identified among ever smokers (rs291231; P = 1.92 × 10) approached statistical significance for replication in admixed populations of African ancestry, and a novel SNP for COPD in PDZD2 (rs7709630; P = 1.56 × 10) regionally replicated. In addition, loci previously identified for lung function in European samples were associated in Hispanic/Latino participants in the Hispanic Community Health Study/Study of Latinos at the genome-wide significance level. CONCLUSIONS: We identified novel signals for lung function and COPD in a Hispanic/Latino cohort. Including admixed populations when performing genetic studies may identify variants contributing to genetic etiologies of COPD.
Miller ER, Putman RK, Vivero M, Hung Y, Araki T, Nishino M, Washko GR, Rosas IO, Hatabu H, Sholl LM, Hunninghake GM. Histopathology of Interstitial Lung Abnormalities in the Context of Lung Nodule Resections. Am J Respir Crit Care Med 2018;197(7):955-958.
Kinney GL, Santorico SA, Young KA, Cho MH, Castaldi PJ, San José Estépar R, Ross JC, Dy JG, Make BJ, Regan EA, Lynch DA, Everett DC, Lutz SM, Silverman EK, Washko GR, Crapo JD, Hokanson JE. Identification of Chronic Obstructive Pulmonary Disease Axes That Predict All-Cause Mortality: The COPDGene Study. Am J Epidemiol 2018;187(10):2109-2116.Abstract
Chronic obstructive pulmonary disease (COPD) is a syndrome caused by damage to the lungs that results in decreased pulmonary function and reduced structural integrity. Pulmonary function testing (PFT) is used to diagnose and stratify COPD into severity groups, and computed tomography (CT) imaging of the chest is often used to assess structural changes in the lungs. We hypothesized that the combination of PFT and CT phenotypes would provide a more powerful tool for assessing underlying morphologic differences associated with pulmonary function in COPD than does PFT alone. We used factor analysis of 26 variables to classify 8,157 participants recruited into the COPDGene cohort between January 2008 and June 2011 from 21 clinical centers across the United States. These factors were used as predictors of all-cause mortality using Cox proportional hazards modeling. Five factors explained 80% of the covariance and represented the following domains: factor 1, increased emphysema and decreased pulmonary function; factor 2, airway disease and decreased pulmonary function; factor 3, gas trapping; factor 4, CT variability; and factor 5, hyperinflation. After more than 46,079 person-years of follow-up, factors 1 through 4 were associated with mortality and there was a significant synergistic interaction between factors 1 and 2 on death. Considering CT measures along with PFT in the assessment of COPD can identify patients at particularly high risk for death.
Sanders KJC, Ash SY, Washko GR, Mottaghy FM, Schols AMWJ. Imaging approaches to understand disease complexity: chronic obstructive pulmonary disease as a clinical model. J Appl Physiol (1985) 2018;124(2):512-520.Abstract
The clinical manifestations of chronic obstructive pulmonary disease (COPD) reflect an aggregate of multiple pulmonary and extrapulmonary processes. It is increasingly clear that full assessment of these processes is essential to characterize disease burden and to tailor therapy. Medical imaging has advanced such that it is now possible to obtain in vivo insight in the presence and severity of lung disease-associated features. In this review, we have assembled data from multiple disciplines of medical imaging research to review the role of imaging in characterization of COPD. Topics include imaging of the lungs, body composition, and extrapulmonary tissue metabolism. The primary focus is on imaging modalities that are widely available in clinical care settings and that potentially contribute to describing COPD heterogeneity and enhance our insight in underlying pathophysiological processes and their structural and functional effects.
de la Hoz RE, Liu X, Doucette JT, Reeves AP, Bienenfeld LA, Wisnivesky JP, Celedón JC, Lynch DA, San José Estépar R. Increased Airway Wall Thickness is Associated with Adverse Longitudinal First-Second Forced Expiratory Volume Trajectories of Former World Trade Center workers. Lung 2018;196(4):481-489.Abstract
RATIONALE: Occupational exposures at the WTC site after September 11, 2001 have been associated with several presumably inflammatory lower airway diseases. In this study, we describe the trajectories of expiratory air flow decline, identify subgroups with adverse progression, and investigate the association of a quantitative computed tomography (QCT) imaging measurement of airway wall thickness, and other risk factors for adverse progression. METHODS: We examined the trajectories of expiratory air flow decline in a group of 799 former WTC workers and volunteers with QCT-measured (with two independent systems) wall area percent (WAP) and at least 3 periodic spirometries. We calculated individual regression lines for first-second forced expiratory volume (FEV), identified subjects with rapidly declining and increasing ("gainers"), and compared them to subjects with normal and "stable" FEV decline. We used multivariate logistic regression to model decliner vs. stable trajectories. RESULTS: The mean longitudinal FEVslopes for the entire study population, and its stable, decliner, and gainer subgroups were, respectively, - 35.8, - 8, - 157.6, and + 173.62 ml/year. WAP was associated with "decliner" status (OR 1.08, 95% CI 1.02, 1.14, per 5% increment) compared to stable. Age, weight gain, baseline FEV percent predicted, bronchodilator response, and pre-WTC occupational exposures were also significantly associated with accelerated FEV decline. Analyses of gainers vs. stable subgroup showed WAP as a significant predictor in unadjusted but not consistently in adjusted analyses. CONCLUSIONS: The apparent normal age-related rate of FEV decline results from averaging widely divergent trajectories. WAP is significantly associated with accelerated air flow decline in WTC workers.
Ash SY, Harmouche R, Ross JC, Diaz AA, Rahaghi FN, Vegas Sanchez-Ferrero G, Putman RK, Hunninghake GM, Onieva Onieva J, Martinez FJ, Choi AM, Bowler RP, Lynch DA, Hatabu H, Bhatt SP, Dransfield MT, Wells MJ, Rosas IO, Estepar RSJ, Washko GR. Interstitial Features at Chest CT Enhance the Deleterious Effects of Emphysema in the COPDGene Cohort. Radiology 2018;288(2):600-609.Abstract
Purpose To determine if interstitial features at chest CT enhance the effect of emphysema on clinical disease severity in smokers without clinical pulmonary fibrosis. Materials and Methods In this retrospective cohort study, an objective CT analysis tool was used to measure interstitial features (reticular changes, honeycombing, centrilobular nodules, linear scar, nodular changes, subpleural lines, and ground-glass opacities) and emphysema in 8266 participants in a study of chronic obstructive pulmonary disease (COPD) called COPDGene (recruited between October 2006 and January 2011). Additive differences in patients with emphysema with interstitial features and in those without interstitial features were analyzed by using t tests, multivariable linear regression, and Kaplan-Meier analysis. Multivariable linear and Cox regression were used to determine if interstitial features modified the effect of continuously measured emphysema on clinical measures of disease severity and mortality. Results Compared with individuals with emphysema alone, those with emphysema and interstitial features had a higher percentage predicted forced expiratory volume in 1 second (absolute difference, 6.4%; P < .001), a lower percentage predicted diffusing capacity of lung for carbon monoxide (DLCO) (absolute difference, 7.4%; P = .034), a 0.019 higher right ventricular-to-left ventricular (RVLV) volume ratio (P = .029), a 43.2-m shorter 6-minute walk distance (6MWD) (P < .001), a 5.9-point higher St George's Respiratory Questionnaire (SGRQ) score (P < .001), and 82% higher mortality (P < .001). In addition, interstitial features modified the effect of emphysema on percentage predicted DLCO, RVLV volume ratio, 6WMD, SGRQ score, and mortality (P for interaction < .05 for all). Conclusion In smokers, the combined presence of interstitial features and emphysema was associated with worse clinical disease severity and higher mortality than was emphysema alone. In addition, interstitial features enhanced the deleterious effects of emphysema on clinical disease severity and mortality.
Boueiz A, Chang Y, Cho MH, Washko GR, San José Estépar R, Bowler RP, Crapo JD, DeMeo DL, Dy JG, Silverman EK, Castaldi PJ. Lobar Emphysema Distribution Is Associated With 5-Year Radiological Disease Progression. Chest 2018;153(1):65-76.Abstract
BACKGROUND: Emphysema has considerable variability in its regional distribution. Craniocaudal emphysema distribution is an important predictor of the response to lung volume reduction. However, there is little consensus regarding how to define upper lobe-predominant and lower lobe-predominant emphysema subtypes. Consequently, the clinical and genetic associations with these subtypes are poorly characterized. METHODS: We sought to identify subgroups characterized by upper-lobe or lower-lobe emphysema predominance and comparable amounts of total emphysema by analyzing data from 9,210 smokers without alpha-1-antitrypsin deficiency in the Genetic Epidemiology of COPD (COPDGene) cohort. CT densitometric emphysema was measured in each lung lobe. Random forest clustering was applied to lobar emphysema variables after regressing out the effects of total emphysema. Clusters were tested for association with clinical and imaging outcomes at baseline and at 5-year follow-up. Their associations with genetic variants were also compared. RESULTS: Three clusters were identified: minimal emphysema (n = 1,312), upper lobe-predominant emphysema (n = 905), and lower lobe-predominant emphysema (n = 796). Despite a similar amount of total emphysema, the lower-lobe group had more severe airflow obstruction at baseline and higher rates of metabolic syndrome compared with subjects with upper-lobe predominance. The group with upper-lobe predominance had greater 5-year progression of emphysema, gas trapping, and dyspnea. Differential associations with known COPD genetic risk variants were noted. CONCLUSIONS: Subgroups of smokers defined by upper-lobe or lower-lobe emphysema predominance exhibit different functional and radiological disease progression rates, and the upper-lobe predominant subtype shows evidence of association with known COPD genetic risk variants. These subgroups may be useful in the development of personalized treatments for COPD.
Ross JC, Castaldi PJ, Cho MH, Hersh CP, Rahaghi FN, Sánchez-Ferrero GV, Parker MM, Litonjua AA, Sparrow D, Dy JG, Silverman EK, Washko GR, San José Estépar R. Longitudinal Modeling of Lung Function Trajectories in Smokers with and without Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2018;198(8):1033-1042.Abstract
RATIONALE: The relationship between longitudinal lung function trajectories, chest computed tomography (CT) imaging, and genetic predisposition to chronic obstructive pulmonary disease (COPD) has not been explored. OBJECTIVES: 1) To model trajectories using a data-driven approach applied to longitudinal data spanning adulthood in the Normative Aging Study (NAS), and 2) to apply these models to demographically similar subjects in the COPDGene (Genetic Epidemiology of COPD) Study with detailed phenotypic characterization including chest CT. METHODS: We modeled lung function trajectories in 1,060 subjects in NAS with a median follow-up time of 29 years. We assigned 3,546 non-Hispanic white males in COPDGene to these trajectories for further analysis. We assessed phenotypic and genetic differences between trajectories and across age strata. MEASUREMENTS AND MAIN RESULTS: We identified four trajectories in NAS with differing levels of maximum lung function and rate of decline. In COPDGene, 617 subjects (17%) were assigned to the lowest trajectory and had the greatest radiologic burden of disease (P < 0.01); 1,283 subjects (36%) were assigned to a low trajectory with evidence of airway disease preceding emphysema on CT; 1,411 subjects (40%) and 237 subjects (7%) were assigned to the remaining two trajectories and tended to have preserved lung function and negligible emphysema. The genetic contribution to these trajectories was as high as 83% (P = 0.02), and membership in lower lung function trajectories was associated with greater parental histories of COPD, decreased exercise capacity, greater dyspnea, and more frequent COPD exacerbations. CONCLUSIONS: Data-driven analysis identifies four lung function trajectories. Trajectory membership has a genetic basis and is associated with distinct lung structural abnormalities.
Suh YJ, McDonald M-LN, Washko GR, Carolan BJ, Bowler RP, Lynch DA, Kinney GL, Bon JM, Cho MH, Crapo JD, Regan EA. Lung, Fat and Bone: Increased Adiponectin Associates with the Combination of Smoking-Related Lung Disease and Osteoporosis. Chronic Obstr Pulm Dis 2018;5(2):134-143.Abstract
Adiponectin has been proposed as a biomarker of disease severity and progression in chronic obstructive pulmonary disease (COPD) and associated with spirometry-defined COPD and with computed tomography (CT)-measured emphysema. Increased adiponectin plays a role in other diseases including diabetes/metabolic syndrome, cardiovascular disease and osteoporosis. Previous studies of adiponectin and COPD have not assessed the relationship of adiponectin to airway disease in smokers and have not evaluated the effect of other comorbid diseases on the relationship of adiponectin and lung disease. We postulated that adiponectin levels would associate with both airway disease and emphysema in smokers with and without COPD, and further postulated that body composition and the comorbid diseases of osteoporosis, cardiovascular disease and diabetes might influence adiponectin levels. Current and former smokers from the COPD Genetic Epidemiology study (COPDGene) (n= 424) were assigned to 4 groups based on CT lung characteristics and volumetric Bone Density (vBMD). Emphysema (% low attenuation area at -950) and airway disease (Wall area %) were used to assess smoking-related lung disease (SRLD). Group 1) Normal Lung with Normal vBMD; Group 2) Normal Lung and Osteoporosis; Group 3) SRLD with Normal vBMD; Group 4) SRLD with Osteoporosis. Cardiovascular disease (CVD), diabetes, C-reactive protein (CRP) and T-cadherin (soluble receptor for adiponectin) levels were defined for each group. Body composition was derived from chest CT. Multivariable regression assessed effects of emphysema, wall area %, bone density, comorbid diseases and other key factors on log adiponectin. Group 4, SRLD with Osteoporosis, had significantly higher adiponectin levels compared to other groups and the effect persisted in adjusted models. Systemic inflammation (by CRP) was associated with SRLD in Groups 3 and 4 but not with osteoporosis alone. In regression models, lower bone density and worse emphysema were associated with higher adiponectin. Airway disease was associated with higher adiponectin levels when T-cadherin was added to the model. Male gender, greater muscle and fat were associated with lower adiponectin. Adiponectin is increased with both airway disease and emphysema in smokers. Bone density, and fat and muscle composition are all significant factors predicting adiponectin that should be considered when it is used as a biomarker of COPD. Increased adiponectin from chronic inflammation may play a role in the progression of bone loss in COPD and other lung diseases.
Onieva Onieva J, Serrano GG, Young TP, Washko GR, Carbayo MJL, San José Estépar R. Multiorgan structures detection using deep convolutional neural networks. Proc SPIE Int Soc Opt Eng 2018;10574Abstract
Many automatic image analysis algorithms in medical imaging require a good initialization to work properly. A similar problem occurs in many imaging-based clinical workflows, which depend on anatomical landmarks. The localization of anatomic structures based on a defined context provides with a solution to that problem, which turns out to be more challenging in medical imaging where labeled images are difficult to obtain. We propose a two-stage process to detect and regress 2D bounding boxes of predefined anatomical structures based on a 2D surrounding context. First, we use a deep convolutional neural network (DCNN) architecture to detect the optimal slice where an anatomical structure is present, based on relevant landmark features. After this detection, we employ a similar architecture to perform a 2D regression with the aim of proposing a bounding box where the structure is encompassed. We trained and tested our system for 57 anatomical structures defined in axial, sagittal and coronal planes with a dataset of 504 labeled Computed Tomography (CT) scans. We compared our method with a well-known object detection algorithm (Viola Jones) and with the inter-rater error for two human experts. Despite the relatively small number of scans and the exhaustive number of structures analyzed, our method obtained promising and consistent results, which proves our architecture very generalizable to other anatomical structures.
Ramos-Llorden G, Vegas-Sanchez-Ferrero G, Bjork M, Vanhevel F, Parizel PM, Estepar RSJ, den Dekker AJ, Sijbers J. NOVIFAST: A Fast Algorithm for Accurate and Precise VFA MRI Mapping. IEEE Trans Med Imaging 2018;37(11):2414-2427.Abstract
In quantitative magnetic resonance mapping, the variable flip angle (VFA) steady state spoiled gradient recalled echo (SPGR) imaging technique is popular as it provides a series of high resolution weighted images in a clinically feasible time. Fast, linear methods that estimate maps from these weighted images have been proposed, such as DESPOT1 and iterative re-weighted linear least squares. More accurate, non-linear least squares (NLLS) estimators are in play, but these are generally much slower and require careful initialization. In this paper, we present NOVIFAST, a novel NLLS-based algorithm specifically tailored to VFA SPGR mapping. By exploiting the particular structure of the SPGR model, a computationally efficient, yet accurate and precise map estimator is derived. Simulation and in vivo human brain experiments demonstrate a twenty-fold speed gain of NOVIFAST compared with conventional gradient-based NLLS estimators while maintaining a high precision and accuracy. Moreover, NOVIFAST is eight times faster than the efficient implementations of the variable projection (VARPRO) method. Furthermore, NOVIFAST is shown to be robust against initialization.
Copeland CR, Nath H, Terry NLJ, Wilson CG, Kim Y-I, Lynch DA, Bodduluri S, Wells MJ, Dransfield MT, Díaz AA, Washko GR, Foreman MG, Bhatt SP. Paratracheal Paraseptal Emphysema and Expiratory Central Airway Collapse in Smokers. Ann Am Thorac Soc 2018;15(4):479-484.Abstract
RATIONALE: Expiratory central airway collapse is associated with respiratory morbidity independent of underlying lung disease. However, not all smokers develop expiratory central airway collapse, and the etiology of expiratory central airway collapse in adult smokers is unclear. Paraseptal emphysema in the paratracheal location, by untethering airway walls, may predispose smokers to developing expiratory central airway collapse. OBJECTIVES: To evaluate whether paratracheal paraseptal emphysema is associated with expiratory central airway collapse. METHODS: We analyzed paired inspiratory and expiratory computed tomography scans from participants enrolled in a multicenter study (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease) of smokers aged 45 to 80 years. Expiratory central airway collapse was defined as greater than or equal to 50% reduction in cross-sectional area of the trachea during expiration. In a nested case-control design, participants with and without expiratory central airway collapse were included in a 1:2 fashion, and inspiratory scans were further analyzed using the Fleischner Society criteria for presence of centrilobular emphysema, paraseptal emphysema, airway wall thickening, and paratracheal paraseptal emphysema (maximal diameter ≥ 0.5 cm). RESULTS: A total of 1,320 patients were included, 440 with and 880 without expiratory central airway collapse. Those with expiratory central airway collapse were older, had higher body mass index, and were less likely to be men or current smokers. Paratracheal paraseptal emphysema was more frequent in those with expiratory central airway collapse than control subjects (16.6 vs. 11.8%; P = 0.016), and after adjustment for age, race, sex, body mass index, smoking pack-years, and forced expiratory volume in 1 second, paratracheal paraseptal emphysema was independently associated with expiratory central airway collapse (adjusted odds ratio, 1.53; 95% confidence interval, 1.18-1.98; P = 0.001). Furthermore, increasing size of paratracheal paraseptal emphysema (maximal diameter of at least 1 cm and 1.5 cm) was associated with greater odds of expiratory central airway collapse (adjusted odds ratio, 1.63; 95% confidence interval, 1.18-2.25; P = 0.003 and 1.77; 95% confidence interval, 1.19-2.64; P = 0.005, respectively). CONCLUSIONS: Paraseptal emphysema adjacent to the trachea is associated with expiratory central airway collapse. The identification of this risk factor on inspiratory scans should prompt further evaluation for expiratory central airway collapse. Clinical trial registered with (NCT 00608764).
Diaz AA, Martinez CH, Harmouche R, Young TP, McDonald M-L, Ross JC, Han ML, Bowler R, Make B, Regan EA, Silverman EK, Crapo J, Boriek AM, Kinney GL, Hokanson JE, Estepar RSJ, Washko GR. Pectoralis muscle area and mortality in smokers without airflow obstruction. Respir Res 2018;19(1):62.Abstract
BACKGROUND: Low muscle mass is associated with increased mortality in the general population but its prognostic value in at-risk smokers, those without expiratory airflow obstruction, is unknown. We aimed to test the hypothesis that reduced muscle mass is associated with increased mortality in at-risk smokers. METHODS: Measures of both pectoralis and paravertebral erector spinae muscle cross-sectional area (PMA and PVMA, respectively) as well as emphysema on chest computed tomography (CT) scans were performed in 3705 current and former at-risk smokers (≥10 pack-years) aged 45-80 years enrolled into the COPDGene Study between 2008 and 2013. Vital status was ascertained through death certificate. The association between low muscle mass and mortality was assessed using Cox regression analysis. RESULTS: During a median of 6.5 years of follow-up, 212 (5.7%) at-risk smokers died. At-risk smokers in the lowest (vs. highest) sex-specific quartile of PMA but not PVMA had 84% higher risk of death in adjusted models for demographics, smoking, dyspnea, comorbidities, exercise capacity, lung function, emphysema on CT, and coronary artery calcium content (hazard ratio [HR] 1.85 95% Confidence interval [1.14-3.00] P = 0.01). Results were consistent when the PMA index (PMA/height) was used instead of quartiles. The association between PMA and death was modified by smoking status (P = 0.04). Current smokers had a significantly increased risk of death (lowest vs. highest PMA quartile, HR 2.25 [1.25-4.03] P = 0.007) while former smokers did not. CONCLUSIONS: Low muscle mass as measured on chest CT scans is associated with increased mortality in current smokers without airflow obstruction. TRIAL REGISTRATION: NCT00608764.
Washko GR. POINT: Should Chest CT Be Part of Routine Clinical Care for COPD? Yes. Chest 2018;154(6):1276-1278.