Anomalies in MERRA-2 & AWS Weather Data over the East Antarctic Plateau

In 2018, scientists published an analysis of recent coldest temperatures recorded on Earth. Temperatures of the snow surface in the East Antarctica Plateau were observed to reach -98.0 &deg;C from thermal emission measured through satellite thermal-band derived data. The study estimated about -94&deg;C to -95&deg;C (&plusmn;4&deg;C) air temperature at 2 meters above the surface. These locations and events appear to be several degrees colder than the historical low 2 m air temperature record of &minus;89.2&deg;C at Vostok station reported in July of 1983. The discovery inspired this investigation of a discrepancy between the MERRA-2 model data and in situ data from two Automatic Weather Stations (AWS) known as PlateauB (78&deg;39' S, 35&deg;38' E, ~3620 m a.s.l.) and Pole of Inaccessibility (82&deg;07' S, 55&deg;02' E, ~3730 m a.s.l.), located close to the coldest recorded temperatures discussed by Scambos et al. Comparisons of year by year daily mean 2-meter air temperatures from AWS and climate reanalysis data (NASA&rsquo;s MERRA-2 data set) yielded high overall correlations (most R &ge; 0.84), but consistently MERRA-2 temperatures did not reach the lowest temperatures (below -65&deg;C) during the colder months (April-Sep). During these months, which are periods of low or no sunlight, the difference between MERRA-2 2-meter air temperatures and observed AWS 2-meter air temperature varied systematically with temperature, with the difference being greatest (up to ~ -12&deg;C) at the coldest AWS-recorded conditions. Correlations for months of daily mean AWS 2-meter temperatures with the difference between AWS and MERRA-2 temperatures are higher for the cold months (April-September; R=0.55-0.91) than the sunlit warmer months (October-March, R=0.13-0.87). Moreover, at the warm end of the cold-month monthly trends, MERRA-2 temperatures were warmer by several degrees (~ 4&deg;C&deg;C) than the observed AWS temperatures. We then examined the difference between AWS Temperatures and wind speeds (data from MERRA-2). The lowest temperatures occur during periods of low wind speed (&lt; 2 ms-1) while the warmest winter days at these sites are periods of high wind speeds (&gt; 10 ms-1). During these periods of high wind, the wind direction is in the direction of gravitationally-driven drainage (i.e., katabatic winds), which are closely tied to the intensity of the near-surface thermal inversion that is a common occurrence over ice sheets (9). MERRA-2 appears to not capture the high variability of the inversion layer gradient. We hypothesize that slow winds result in a strong inversion, and thus a steep temperature gradient with lowest temperatures near the surface; that moderate winds (4-8 ms-1) in an inversion is close to what the MERRA-2 model estimates, thus with consistent temperatures between MERRA-2 and the AWS; and that fast winds result in the inversion being disrupted or overcome due to turbulent airflow and downward mixing of warm air, thus resulting in temperatures higher than the MERRA-2 estimate. Studying, characterizing, and describing such extremely cold temperatures and regions can provide insight into our understanding of polar climate, the interaction of the atmosphere and ice sheet areas, and provides analogies to other locations of extremely cold temperatures governed by similar processes in our solar system (e.g., Mars&rsquo; polar regions).</p

Multidecadal observations of the Antarctic ice sheet from restored analog radar records.

Airborne radar sounding can measure conditions within and beneath polar ice sheets. In Antarctica, most digital radar-sounding data have been collected in the last 2 decades, limiting our ability to understand processes that govern longer-term ice-sheet behavior. Here, we demonstrate how analog radar data collected over 40 y ago in Antarctica can be combined with modern records to quantify multidecadal changes. Specifically, we digitize over 400,000 line kilometers of exploratory Antarctic radar data originally recorded on 35-mm optical film between 1971 and 1979. We leverage the increased geometric and radiometric resolution of our digitization process to show how these data can be used to identify and investigate hydrologic, geologic, and topographic features beneath and within the ice sheet. To highlight their scientific potential, we compare the digitized data with contemporary radar measurements to reveal that the remnant eastern ice shelf of Thwaites Glacier in West Antarctica had thinned between 10 and 33% between 1978 and 2009. We also release the collection of scanned radargrams in their entirety in a persistent public archive along with updated geolocation data for a subset of the data that reduces the mean positioning error from 5 to 2.5 km. Together, these data represent a unique and renewed extensive, multidecadal historical baseline, critical for observing and modeling ice-sheet change on societally relevant timescales

Ants defend coffee from berry borer colonization

Ants frequently prevent herbivores from damaging plants. In agroecosystems they may provide pest control services, although their contributions are not always appreciated. Here we compared the ability of eight ant species to prevent the coffee berry borer from colonizing coffee berries with a field exclusion experiment. We removed ants from one branch (exclusion) and left ants to forage on a second branch (control) before releasing 20 berry borers on each branch. After 24 h, six of eight species had significantly reduced the number of berries bored by the berry borer compared to exclusion treatment branches. While the number of berries per branch was a significant covariate explaining the number of berries bored, ant activity (that varied greatly among species) was not a significant factor in models. This study is the first field experiment to provide evidence that a diverse group of ant species limit the berry borer from colonizing coffee berries. © 2013 International Organization for Biological Control (IOBC)

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

BRCA1 and BRCA2 pathogenic sequence variants in women of African origin or ancestry.

BRCA1 and BRCA2 (BRCA1/2) pathogenic sequence variants (PSVs) confer elevated risks of multiple cancers. However, most BRCA1/2 PSVs reports focus on European ancestry individuals. Knowledge of the PSV distribution in African descent individuals is poorly understood. We undertook a systematic review of the published literature and publicly available databases reporting BRCA1/2 PSVs also accessed the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) database to identify African or African descent individuals. Using these data, we inferred which of the BRCA PSVs were likely to be of African continental origin. Of the 43,817 BRCA1/2 PSV carriers in the CIMBA database, 469 (1%) were of African descent. Additional African descent individuals were identified in public databases (n = 291) and the literature (n = 601). We identified 164 unique BRCA1 and 173 unique BRCA2 PSVs in individuals of African ancestry. Of these, 83 BRCA1 and 91 BRCA2 PSVs are of likely or possible African origin. We observed numerous differences in the distribution of PSV type and function in African origin versus non-African origin PSVs. Research in populations of African ancestry with BRCA1/2 PSVs is needed to provide the information needed for clinical management and decision-making in African descent individuals worldwide

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

Integrated genomic characterization of oesophageal carcinoma

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity