Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment. Tumor-infiltrating lymphocytes (TILs) were identified from standard pathology cancer images by a deep-learning-derived \u201ccomputational stain\u201d developed by Saltz et al. They processed 5,202 digital images from 13 cancer types. Resulting TIL maps were correlated with TCGA molecular data, relating TIL content to survival, tumor subtypes, and immune profiles

On the structure and propagation of internal solitary waves generated at the Mascarene Plateau in the Indian Ocean

The Mascarene Plateau in the Western Indian Ocean is identified as a new internal solitary wave hotspot. Satellite SAR images show that powerful internal waves radiate both to the West and East from a central sill near 12.5° S, 61° E between the Saya de Malha and Nazareth Banks. To first order, the waves appear in tidally generated packets on both sides of the sill, and those on the western side have crest-lengths in excess of 350 km, amongst the longest yet recorded anywhere in the world’s oceans. The propagation characteristics of these internal waves are well described by first mode linear waves interacting with background shear taken from the westward-flowing South Equatorial Current (SEC), a large part of which flows through the sill in question. Analysis of the timings and locations of the packets indicates that both the westward- and eastward- travelling waves are generated from the western side of the sill at the predicted time of maximum tidal flow to the West. The linear generation mechanism is therefore proposed as the splitting of a large lee wave that forms on the western side of the sill, in a similar manner to that already identified for the shelf break generation of internal waves in the northern Bay of Biscay. While lee waves should form on either side of the sill in an oscillatory tidal flow, that on the western side would be expected to be much larger than that on the eastern side because of a superposition of the tidal flow and the steady westward flow of the SEC. The existence of a large lee wave at the right time in the tidal cycle is then finally confirmed by direct observations. Our study also confirms the existence of second mode internal waves that form on the western side of the sill and travel across the sill towards the East

ASIRI: An ocean-atmosphere initiative for bay of Bengal

An observation and modeling campaign in the Bay of Bengal is aimed at studying upper-ocean and lower-atmosphere processes and interactions in relation to Indian Ocean monsoons