The first confirmed superoutburst of the SU UMa type dwarf nova SDSS J083931.35+282824.0

We report unfiltered CCD photometry of the first confirmed superoutburst of the recently discovered dwarf nova, SDSS J083931.35+282824.0 in April 2010. From a quiescence magnitude of ~19.8 it rose to 14.0, an outburst amplitude of at least 5.8 magnitudes. Only the plateau phase of the outburst was observed during which superhumps with peak-to-peak amplitude of up to 0.28 magnitudes were present, confirming this to be an SU UMa type dwarf nova. The mean superhump period was Psh = 0.07836(2) during the first 3 days and this subsequently decreased to 0.07800(3) d. Analysis of the data revealed tentative evidence for an orbital period Porb = 0.07531(25) d. The fractional superhump period excess was epsilon = 0.039(6), which is consistent with other dwarf novae of similar orbital period.Comment: 12 pages, 3 figures. Accepted for publication in the Journal of the British Astronomical Associatio

Discourse comprehension in L2: Making sense of what is not explicitly said

Using ERPs, we tested whether L2 speakers can integrate multiple sources of information (e.g., semantic, pragmatic information) during discourse comprehension. We presented native speakers and L2 speakers with three-sentence scenarios in which the final sentence was highly causally related, intermediately related, or causally unrelated to its context; its interpretation therefore required simple or complex inferences. Native speakers revealed a gradual N400-like effect, larger in the causally unrelated condition than in the highly related condition, and falling in-between in the intermediately related condition, replicating previous results. In the crucial intermediately related condition, L2 speakers behaved like native speakers, however, showing extra processing in a later time-window. Overall, the results show that, when reading, L2 speakers are able to process information from the local context and prior information (e.g., world knowledge) to build global coherence, suggesting that they process different sources of information to make inferences online during discourse comprehension, like native speakers.This work was supported by grants from the Spanish Government (PSI2011-23033, CONSOLIDER-INGENIO2010 CSD2007-00048, ECO2011-25295, and ECO2010-09555-E), from the Catalan Government (SGR 2009-1521) and from the Grup de Recerca en Neurociència Cognitiva (GRNC) - 2014SGR1210. It has also received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 613465

IM Normae: The Death Spiral of a Cataclysmic Variable?

We present a study of the orbital light curves of the recurrent nova IM Normae since its 2002 outburst. The broad "eclipses" recur with a 2.46 hour period, which increases on a timescale of 1.28(16)x10^6 years. Under the assumption of conservative mass-transfer, this suggests a rate near 10^-7 M_sol/year, and this agrees with the estimated /accretion/ rate of the postnova, based on our estimate of luminosity. IM Nor appears to be a close match to the famous recurrent nova T Pyxidis. Both stars appear to have very high accretion rates, sufficient to drive the recurrent-nova events. Both have quiescent light curves which suggest strong heating of the low-mass secondary, and very wide orbital minima which suggest obscuration of a large "corona" around the primary. And both have very rapid orbital period increases, as expected from a short-period binary with high mass transfer from the low-mass component. These two stars may represent a final stage of nova -- and cataclysmic-variable -- evolution, in which irradiation-driven winds drive a high rate of mass transfer, thereby evaporating the donor star in a paroxysm of nova outbursts.Comment: PDF, 30 pages, 3 tables, 6 figures; accepted, in press, ApJ; more info at http://cbastro.org

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

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

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