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Biology subjects

Chacko, R.

Publications and source records attributed to Chacko, R..

2 recordsLinked to original sources

DeltaAI: Semi-Autonomous Tissue Grossing Measurements and Recommendations using Neural Radiance Fields for Rapid, Complete Intraoperative Histological Assessment of Tumor Margins

Mohs Micrographic Surgery (MMS) aims to excise cutaneous cancer with real-time margin analysis. However, manual tissue grossing and analysis can be inefficient, so we propose DeltaAI, a novel workflow that utilizes Neural Radiance Fields (NeRF) to enable rapid tissue grossing and generate a 3D model in an augmented reality (AR) environment. In our study, we captured 30-second videos of 17 MMS specimens using a photogrammetry turntable and cellphone camera. Preprocessing the tissues with segmentation models, we created a dataset of 923, 360-degree-view, images per video (17 videos). Using COLMAP, we estimated poses for sparse tissue reconstructions and trained the NeRF model for 3D volumetric tissue renderings. The results demonstrated that DeltaAI generated more accurate and complete 360-degree, 3D tissue renderings compared to previous models, while also achieving significantly faster runtimes. Our proposed semi-autonomous NeRF-based workflow has the potential to enhance the speed of MMS specimen processing, measurement, report generation, and margin assessment. It can inform real-time grossing decisions, automate the export of electronic health record data, and facilitate time-efficient and complete cancer excisions. Moreover, DeltaAI can contribute to the wider adoption of AI technology in clinical settings by improving tissue modeling for manual grossing.

pathology↗

Brief Report: Prognostic relevance of 3q amplification in squamous cell carcinoma of the lung

IntroductionAmplification of 3q is the most common genetic alteration identified in squamous cell carcinoma of the lung (LUSC) with the most frequent amplified region being 3q26-3q28. MethodsIn this analysis, we aim to describe the prognostic relevance of 3q by focusing on a minimal common region (MCR) of amplification within 3q constituted by 25 genes. We analyzed 511 cases of LUSC from The Cancer Genome Atlas (TCGA) and included 476 in the final analysis. ResultsWe identified a 25-gene MCR that was amplified in 221 (44.3%) cases and was associated with better disease specific-survival (DSS) (NR versus 9.25 years; 95% CI [5.24-NR]; log-rank p=0.011) and a progression-free interval (PFI) of 8 years (95% CI [5.1-NR]) versus 4.9 years (95% [3.5-NR]) (Log-rank p=0.020). Multivariable analysis revealed MCR amplification was associated with improved DSS and PFI. ConclusionAmplification of the 25-gene MCR within 3q was present in 44% of this cohort mainly composed of Caucasian patients with early-stage LUSC. This analysis is a strong indicator of the prognostic relevance of the 25-gene MCR within 3q. We are further evaluating its prognostic relevance in a racially diverse patient population with advanced LUSC.

genomics↗