Chemical characteristics of air from differing source regions during the Pacific Exploratory Mission‐Tropics A (PEM‐Tropics A)

Ten‐day backward trajectories are used to determine the origins of air parcels arriving at airborne DC‐8 chemical measurement sites during NASA\u27s Pacific Exploratory Mission‐Tropics A (PEM‐T) that was conducted during August‐October 1996. Those sites at which the air had a common geographical origin and transport history are grouped together, and statistical measures of chemical characteristics are computed. Temporal changes in potential temperature are used to determine whether trajectories experience a significant convective influence during the 10‐day period. Those trajectories that do not experience a significant convective influence are divided into four geographical categories depending on their origins and paths. Air parcels originating over Africa and South America are characterized by enhanced mixing ratios of O3, CO, HNO3, and PAN. The backward trajectories travel at high altitudes (∼10–11 km), covering long distances due to strong upper‐tropospheric westerly winds. The observed enhancement of combustion‐related species is attributed to biomass burning from distant sources to the west, extending even to South America. The relatively large value of Be‐7 probably is due either to less efficient removal of aerosols from upper tropospheric air or to small stratospheric contributions. Aged marine parcels are found to have relatively small concentrations of burning‐related species. Although these trajectories arrive at a wide range of aircraft altitudes, they do not pass over a land mass during the preceding 10‐day period. Air passing over Australia but no other land mass exhibits a combustion signature; however, photochemical product species such as O3 and PAN are less enhanced than in the long‐range transport category. These trajectories travel shorter distances and are at lower altitudes (∼5–8 km) than those reaching Africa and/or South America. The combustion influence on these parcels is attributed to biomass burning emissions injected over Australia. That burning is less widespread than in Africa and South America. Finally, trajectories originating over Southeast Asia appear to receive a weak combustion influence. However, compared to Africa and South America, Southeast Asia has a relatively small incidence of biomass burning. There is little combustion input from Australia due to the high transport altitudes compared to the lower heights of the convection. The Southeast Asian parcels exhibit the greatest NOx to ∑NOi ratio of any category, perhaps due to lightning. Parcels experiencing a significant convective influence also are examined. Most of these parcels pass through widespread, persistent convection along either the South Pacific Convergence Zone or Intertropical Convergence Zone approximately 5 days prior to arriving at the aircraft locations. Thus the category mostly represents marine convection. Mixing ratios of peroxides and acids in the convective category are found to be smaller than in parcels not experiencing convection. Small mixing ratios of Be‐7 and Pb‐210 suggest particle removal by precipitation

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 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

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

Exploring public views on marine litter in Europe: Perceived causes, consequences and pathways to change

Marine litter is a global challenge and society plays an important role via lifestyles and behaviour, including policy support. We analysed public perceptions of marine litter and contributing factors, using data from 1133 respondents across 16 European countries. People reported high levels of concern about marine litter, and the vast majority (95%) reported seeing litter when visiting the coast. The problem was attributed to product and packaging design and behaviour rather than lack of facilities or accidental loss of items. Retailers, industry and government were perceived as most responsible, but also least motivated and competent to reduce marine litter, whereas scientists and environmental groups were perceived as least responsible but most motivated and competent. Regression analyses demonstrated the importance of psychological factors such as values and social norms above socio-demographic variables. These findings are important for communications and interventions to reduce inputs of marine litter to the natural environment

Small Non-coding RNAs Govern Mammary Gland Tumorigenesis

Small non-coding RNAs include siRNA, miRNA, piRNA and snoRNA. The involvement of miRNAs in the regulation of mammary gland tumorigenesis has been widely studied while the role for other small non-coding RNAs remains unclear. Here we summarize the involvement of miRNA in breast cancer onset and progression through regulating the cell cycle and cellular proliferation. The regulation of breast cancer stem cells and tumor regeneration by miRNA is reviewed. In addition, the emerging evidence demonstrating the involvement of piRNA and snoRNA in breast cancer is briefly described