Prediction of Visual Field Progression with Baseline and Longitudinal Structural Measurements Using Deep Learning.

PURPOSE: Identifying glaucoma patients at high risk of progression based on widely available structural data is an unmet task in clinical practice. We test the hypothesis that baseline or serial structural measures can predict visual field (VF) progression with deep learning (DL). DESIGN: Development of a DL algorithm to predict VF progression. METHODS: 3,079 eyes (1,765 patients) with various types of glaucoma and ≥5 VFs, and ≥3 years of follow-up from a tertiary academic center were included. Serial VF mean deviation (MD) rates of change were estimated with linear-regression. VF progression was defined as negative MD slope with p<0.05. A Siamese Neural Network with ResNet-152 backbone pre-trained on ImageNet was designed to predict VF progression using serial optic-disc photographs (ODP), and baseline retinal nerve fiber layer (RNFL) thickness. We tested the model on a separate dataset (427 eyes) with RNFL data from different OCT. The Main Outcome Measure was Area under ROC curve (AUC). RESULTS: Baseline average (SD) MD was 3.4 (4.9)dB. VF progression was detected in 900 eyes (29%). AUC (95% CI) for model incorporating baseline ODP and RNFL thickness was 0.813 (0.757-0.869). After adding the second and third ODPs, AUC increased to 0.860 and 0.894, respectively (p<0.027). This model also had highest AUC (0.911) for predicting fast progression (MD rate <1.0 dB/year). Model's performance was similar when applied to second dataset using RNFL data from another OCT device (AUC=0.893; 0.837-0.948). CONCLUSIONS: DL model predicted VF progression with clinically relevant accuracy using baseline RNFL thickness and serial ODPs and can be implemented as a clinical tool after further validation.

Prediction of Central Visual Field Measures From Macular OCT Volume Scans With Deep Learning.

Purpose: Predict central 10° global and local visual field (VF) measurements from macular optical coherence tomography (OCT) volume scans with deep learning (DL). Methods: This study included 1121 OCT volume scans and 10-2 VFs from 289 eyes (257 patients). Macular scans were used to estimate 10-2 VF mean deviation (MD), threshold sensitivities (TS), and total deviation (TD) values at 68 locations. A three-dimensional (3D) convolutional neural network based on the 3D DenseNet121 architecture was used for prediction. We compared DL predictions to those from baseline linear models. We carried out 10-fold stratified cross-validation to optimize generalizability. The performance of the DL and baseline models was compared based on correlations between ground truth and predicted VF measures and mean absolute error (MAE; ground truth - predicted values). Results: Average (SD) MD was -9.3 (7.7) dB. Average (SD) correlations between predicted and ground truth MD and MD MAE were 0.74 (0.09) and 3.5 (0.4) dB, respectively. Estimation accuracy deteriorated with worsening MD. Average (SD) Pearson correlations between predicted and ground truth TS and MAEs for DL and baseline model were 0.71 (0.05) and 0.52 (0.05) (P < 0.001) and 6.5 (0.6) and 7.5 (0.5) dB (P < 0.001), respectively. For TD, correlation (SD) and MAE (SD) for DL and baseline models were 0.69 (0.02) and 0.48 (0.05) (P < 0.001) and 6.1 (0.5) and 7.8 (0.5) dB (P < 0.001), respectively. Conclusions: Macular OCT volume scans can be used to predict global central VF parameters with clinically relevant accuracy. Translational Relevance: Macular OCT imaging may be used to confirm and supplement central VF findings using deep learning.

Prediction of visual field progression with serial optic disc photographs using deep learning.

AIM: We tested the hypothesis that visual field (VF) progression can be predicted with a deep learning model based on longitudinal pairs of optic disc photographs (ODP) acquired at earlier time points during follow-up. METHODS: 3919 eyes (2259 patients) with ≥2 ODPs at least 2 years apart, and ≥5 24-2 VF exams spanning ≥3 years of follow-up were included. Serial VF mean deviation (MD) rates of change were estimated starting at the fifth visit and subsequently by adding visits until final visit. VF progression was defined as a statistically significant negative slope at two consecutive visits and final visit. We built a twin-neural network with ResNet50-backbone. A pair of ODPs acquired up to a year before the VF progression date or the last VF in non-progressing eyes were included as input. Primary outcome measures were area under the receiver operating characteristic curve (AUC) and model accuracy. RESULTS: The average (SD) follow-up time and baseline VF MD were 8.1 (4.8) years and -3.3 (4.9) dB, respectively. VF progression was identified in 761 eyes (19%). The median (IQR) time to progression in progressing eyes was 7.3 (4.5-11.1) years. The AUC and accuracy for predicting VF progression were 0.862 (0.812-0.913) and 80.0% (73.9%-84.6%). When only fast-progressing eyes were considered (MD rate < -1.0 dB/year), AUC increased to 0.926 (0.857-0.994). CONCLUSIONS: A deep learning model can predict subsequent glaucoma progression from longitudinal ODPs with clinically relevant accuracy. This model may be implemented, after validation, for predicting glaucoma progression in the clinical setting.

Comparison of Ganglion Cell Layer and Ganglion Cell/Inner Plexiform Layer Measures for Detection of Early Glaucoma.

PURPOSE: To test the hypothesis that macular ganglion cell layer (GCL) measurements detect early glaucoma with higher accuracy than ganglion cell/inner plexiform layer (GCIPL) thickness measurements. DESIGN: Cross-sectional study. PARTICIPANTS: The first cohort included 58 glaucomatous eyes with visual field mean deviation (MD) ≥ -6 dB and 125 normal eyes. The second cohort included 72 glaucomatous and 73 normal/glaucoma suspect (GS) eyes with scans able to create GCL/GCIPL deviation maps. METHODS: In the first cohort, 8 × 8 GCL and GCIPL grids were exported and 5 superior and inferior sectors were defined. Global and sectoral GCL and GCIPL measures were used to predict glaucoma. In the second cohort, proportions of scan areas with abnormal (< 5% and < 1% cutoffs) and supernormal (> 95% and > 99% cutoffs) thicknesses on deviation maps were calculated. The extents of GCL and GCIPL abnormal areas were used to predict glaucoma. MAIN OUTCOME MEASURES: Extents of abnormal GCL/GCIPL regions and areas under receiver operating characteristic curves (AUROC) for prediction of glaucoma were compared between GCL or GCIPL measures. RESULTS: The average ± standard deviation MDs were -3.7 ± 1.6 dB and -2.7 ± 1.8 dB in glaucomatous eyes in the first and second cohorts, respectively. Global GCIPL thickness measures (central 18° × 18° macular region) performed better than GCL for early detection of glaucoma (AUROC, 0.928 vs. 0.884, respectively; P = 0.004). Superior and inferior sector 3 thickness measures provided the best discrimination with both GCL and GCIPL (inferior GCL AUROC, 0.860 vs. GCIPL AUROC, 0.916 [P = 0.001]; superior GCL AUROC, 0.916 vs. GCIPL AUROC, 0.900 [P = 0.24]). The extents of abnormal GCL regions at a 1% cutoff in the central elliptical area were 17.5 ± 22.2% and 6.4 ± 10.8% in glaucomatous and normal/GS eyes, respectively, versus 17.0 ± 22.2% and 5.7 ± 10.5%, respectively, for GCIPL (P = 0.06 for GCL and 0.002 for GCIPL). The extents of GCL and GCIPL supernormal regions were mostly similar in glaucomatous and normal eyes. The best performance for prediction of glaucoma in the second cohort was detected at a P value of < 1% within the entire scan for both GCL and GCIPL (AUC, 0.681 vs. 0.668, respectively; P = 0.29). CONCLUSIONS: Macular GCL and GCIPL thicknesses are equivalent for identifying early glaucoma with current OCT technology. This is likely explained by limitations of inner macular layer segmentation and concurrent changes within the inner plexiform layer in early glaucoma.

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site.

Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.

Central Macular Topographic and Volumetric Measures: New Biomarkers for Detection of Glaucoma.

Purpose: To test the hypothesis that newly developed shape measures using optical coherence tomography (OCT) macular volume scans can discriminate patients with perimetric glaucoma from healthy subjects. Methods: OCT structural measures defining macular topography and volume were recently developed based on cubic Bézier curves. We exported macular volume scans from 135 eyes with glaucoma (133 patients) and 155 healthy eyes (85 subjects) and estimated global and quadrant-based measures. The best subset of measures to predict glaucoma was explored with a gradient boost model (GBM) with subsequent logistic regression. Accuracy and area under receiver operating curves (AUC) were the primary metrics. In addition, we separately investigated model performance in 66 eyes with mild glaucoma (mean deviation ≥ -6 dB). Results: Average (±SD) 24-2 mean deviation was -8.2 (±6.1) dB in eyes with glaucoma. The main predictive measures for glaucoma were temporal inferior rim height, nasal inferior pit volume, and temporal inferior pit depth. Lower values for these measures predicted higher risk of glaucoma. Sensitivity, specificity, and AUC for discriminating between healthy and glaucoma eyes were 81.5% (95% CI = 76.6-91.9%), 89.7% (95% CI = 78.7-94.2%), and 0.915 (95% CI = 0.882-0.948), respectively. Corresponding metrics for mild glaucoma were 84.8% (95% CI = 72.1%-95.5%), 85.8% (95% CI = 87.1%-97.4%), and 0.913 (95% CI = 0.867-0.958), respectively. Conclusions: Novel macular shape biomarkers detect early glaucoma with clinically relevant performance. Such biomarkers do not depend on intraretinal segmentation accuracy and may be helpful in eyes with suboptimal macular segmentation. Translational Relevance: Macular shape biomarkers provide valuable information for detection of early glaucoma and may provide additional information beyond thickness measurements.

Prediction of Visual Field Progression from OCT Structural Measures in Moderate to Advanced Glaucoma.

PURPOSE: To test the hypothesis that visual field (VF) progression can be predicted from baseline and longitudinal optical coherence tomography (OCT) structural measurements. DESIGN: Prospective cohort study. METHODS: A total of 104 eyes (104 patients) with ≥3 years of follow-up and ≥5 VF examinations were enrolled. We defined VF progression based on pointwise linear regression on 24-2 VF (≥3 locations with slope less than or equal to -1.0 dB/year and P < .01). We used elastic net logistic regression (ENR) and machine learning to predict VF progression with demographics, baseline circumpapillary retinal nerve fiber layer (RNFL), macular ganglion cell/inner plexiform layer (GCIPL) thickness, and RNFL and GCIPL change rates at central 24 superpixels and 3 eccentricities, 3.4°, 5.5°, and 6.8°, from fovea and hemimaculas. Areas-under-ROC curves (AUC) were used to compare models. RESULTS: Average ± SD follow-up and VF examinations were 4.5 ± 0.9 years and 8.7 ± 1.6, respectively. VF progression was detected in 23 eyes (22%). ENR selected rates of change of superotemporal RNFL sector and GCIPL change rates in 5 central superpixels and at 3.4° and 5.6° eccentricities as the best predictor subset (AUC = 0.79 ± 0.12). Best machine learning predictors consisted of baseline superior hemimacular GCIPL thickness and GCIPL change rates at 3.4° eccentricity and 3 central superpixels (AUC = 0.81 ± 0.10). Models using GCIPL-only structural variables performed better than RNFL-only models. CONCLUSIONS: VF progression can be predicted with clinically relevant accuracy from baseline and longitudinal structural data. Further refinement of proposed models would assist clinicians with timely prediction of functional glaucoma progression and clinical decision making.