An overview of sea state conditions and air-sea fluxes during RaDyO

Refining radiative-transfer modeling capabilities for light transmission through the sea surface requires a more detailed prescription of the sea surface roughness beyond the probability density function of the sea surface slope field. To meet this need, exciting new measurement methodologies now provide the opportunity to enhance present knowledge of sea surface roughness, especially at the microscale. In this context, two intensive field experiments using R/P Floating Instrument Platform were staged within the Office of Naval Research's Radiance in a Dynamic Ocean (RaDyO) field program in the Santa Barbara Channel and in the central Pacific Ocean south of Hawaii. As part of this program, our team gathered and analyzed a comprehensive suite of sea surface roughness measurements designed to provide optimal coverage of fundamental optical distortion processes associated with the air-sea interface. This contribution describes the ensemble of instrumentation deployed. It provides a detailed documentation of the ambient environmental conditions that prevailed during the RaDyO field experiments. It also highlights exciting new sea surface roughness measurement capabilities that underpin a number of the scientific advances resulting from the RaDyO program. For instance, a new polarimetric imaging camera highlights the complex interplay of wind and surface currents in shaping the roughness of the sea surface that suggests the traditional Cox-Munk framework is not sufficient. In addition, the breaking crest length spectral density derived from visible and infrared imagery is shown to be modulated by the development of the wavefield (wave age) and alignment of wind and surface currents at the intermediate (dominant) scale of wave breaking

The Hubble Space Telescope wide field camera 3 early release science data: Panchromatic faint object counts for 0.2-2 μm wavelength

We describe the Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3) Early Release Science (ERS) observations in the Great Observatories Origins Deep Survey (GOODS) South field. The new WFC3 ERS data provide calibrated, drizzled mosaics in the UV filters F225W, F275W, and F336W, as well as in the near-IR filters F098M (Ys ), F125W (J), and F160W (H) with 1-2 HST orbits per filter. Together with the existing HST Advanced Camera for Surveys (ACS) GOODS-South mosaics in the BViz filters, these panchromatic 10-band ERS data cover 40-50arcmin2 at 0.2-1.7 μm in wavelength at 007-015 FWHM resolution and 0090 Multidrizzled pixels to depths of AB≃ 26.0-27.0mag (5σ) for point sources, and AB≃ 25.5-26.5mag for compact galaxies. In this paper, we describe (1) the scientific rationale, and the data taking plus reduction procedures of the panchromatic 10-band ERS mosaics, (2) the procedure of generating object catalogs across the 10 different ERS filters, and the specific star-galaxy separation techniques used, and (3) the reliability and completeness of the object catalogs from the WFC3 ERS mosaics. The excellent 007-015 FWHM resolution of HST/WFC3 and ACS makes star-galaxy separation straightforward over a factor of 10 in wavelength to AB≃ 25-26mag from the UV to the near-IR, respectively. Our main results are: (1) proper motion of faint ERS stars is detected over 6 years at 3.06 ± 0.66masyear-1 (4.6σ), consistent with Galactic structure models; (2) both the Galactic star counts and the galaxy counts show mild but significant trends of decreasing count slopes from the mid-UV to the near-IR over a factor of 10 in wavelength; (3) combining the 10-band ERS counts with the panchromatic Galaxy and Mass Assembly survey counts at the bright end (10mag ≲ AB≲ 20mag) and the Hubble Ultra Deep Field counts in the BVizYsJH filters at the faint end (24mag ≲ AB≲ 30mag) yields galaxy counts that are well measured over the entire flux range 10mag ≲ AB≲ 30mag for 0.2-2 μm in wavelength; (4) simple luminosity+density evolution models can fit the galaxy counts over this entire flux range. However, no single model can explain the counts over this entire flux range in all 10 filters simultaneously. More sophisticated models of galaxy assembly are needed to reproduce the overall constraints provided by the current panchromatic galaxy counts for 10mag ≲ AB≲ 30mag over a factor of 10 in wavelength

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

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 tumorinfiltrating 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

Defining the Middle Corona

International audienceAbstract The middle corona, the region roughly spanning heliocentric distances from 1.5 to 6 solar radii, encompasses almost all of the influential physical transitions and processes that govern the behavior of coronal outflow into the heliosphere. The solar wind, eruptions, and flows pass through the region, and they are shaped by it. Importantly, the region also modulates inflow from above that can drive dynamic changes at lower heights in the inner corona. Consequently, the middle corona is essential for comprehensively connecting the corona to the heliosphere and for developing corresponding global models. Nonetheless, because it is challenging to observe, the region has been poorly studied by both major solar remote-sensing and in-situ missions and instruments, extending back to the Solar and Heliospheric Observatory (SOHO) era. Thanks to recent advances in instrumentation, observational processing techniques, and a realization of the importance of the region, interest in the middle corona has increased. Although the region cannot be intrinsically separated from other regions of the solar atmosphere, there has emerged a need to define the region in terms of its location and extension in the solar atmosphere, its composition, the physical transitions that it covers, and the underlying physics believed to shape the region. This article aims to define the middle corona, its physical characteristics, and give an overview of the processes that occur there

A high-precision near-infrared survey for radial velocity variable low-mass stars using CSHELL and a methane gas cell

We present the results of a precise near-infrared (NIR) radial velocity (RV) survey of 32 low-mass stars with spectral types K2-M4 using CSHELL at the NASA InfraRed Telescope Facility in the K band with an isotopologue methane gas cell to achieve wavelength calibration and a novel, iterative RV extraction method. We surveyed 14 members of young (≈25-150 Myr) moving groups, the young field star ϵ Eridani, and 18 nearby (<25 pc) low-mass stars and achieved typical single-measurement precisions of 8-15 m s-1with a long-term stability of 15-50 m s-1 over longer baselines. We obtain the best NIR RV constraints to date on 27 targets in our sample, 19 of which were never followed by high-precision RV surveys. Our results indicate that very active stars can display long-term RV variations as low as ∼25-50 m s-1 at ≈2.3125 μm, thus constraining the effect of jitter at these wavelengths. We provide the first multiwavelength confirmation of GJ 876 bc and independently retrieve orbital parameters consistent with previous studies. We recovered RV variabilities for HD 160934 AB and GJ 725 AB that are consistent with their known binary orbits, and nine other targets are candidate RV variables with a statistical significance of 3σ-5σ. Our method, combined with the new iSHELL spectrograph, will yield long-term RV precisions of ≲5 m s-1 in the NIR, which will allow the detection of super-Earths near the habitable zone of mid-M dwarfs