A celestial gamma-ray foreground due to the albedo of small solar system bodies and a remote probe of the interstellar cosmic ray spectrum

We calculate the gamma-ray albedo flux from cosmic-ray (CR) interactions with the solid rock and ice in Main Belt asteroids (MBAs), Jovian and Neptunian Trojan asteroids, and Kuiper Belt objects (KBOs) using the Moon as a template. We show that the gamma-ray albedo for the Main Belt, Trojans, and Kuiper Belt strongly depends on the small-body size distribution of each system. Based on an analysis of the Energetic Gamma Ray Experiment Telescope (EGRET) data we infer that the diffuse emission from the MBAs, Trojans, and KBOs has an integrated flux of less than ~6x10^{-6} cm^{-2} s^{-1} (100-500 MeV), which corresponds to ~12 times the Lunar albedo, and may be detectable by the forthcoming Gamma Ray Large Area Space Telescope (GLAST). If detected by GLAST, it can provide unique direct information about the number of small bodies in each system that is difficult to assess by any other method. Additionally, the KBO albedo flux can be used to probe the spectrum of CR nuclei at close-to-interstellar conditions. The orbits of MBAs, Trojans, and KBOs are distributed near the ecliptic, which passes through the Galactic center and high Galactic latitudes. Therefore, the asteroid gamma-ray albedo has to be taken into account when analyzing weak gamma-ray sources close to the ecliptic, especially near the Galactic center and for signals at high Galactic latitudes, such as the extragalactic gamma-ray emission. The asteroid albedo spectrum also exhibits a 511 keV line due to secondary positrons annihilating in the rock. This may be an important and previously unrecognized celestial foreground for the INTErnational Gamma-Ray Astrophysics Laboratory (INTEGRAL) observations of the Galactic 511 keV line emission including the direction of the Galactic center.Comment: 10 pages, 5 figures, 1 table, emulateapj.cls; ApJ in press. Calculations extended to include Jovian and Neptunian Trojan groups, and Centaurs, in addition to Main Belt Asteroids and Kuiper Belt Objects. Many other considerable change

Contribution of nuclei accelerated by gamma-ray pulsars to cosmic rays in the Galaxy

We consider the galactic population of gamma-ray pulsars as possible sources of cosmic rays at and just above the ``knee'' in the observed cosmic ray spectrum at $10^{15}$--$10^{16}$ eV. We suggest that iron nuclei may be accelerated in the outer gaps of pulsars, and then suffer partial photo-disintegration in the non-thermal radiation fields of the outer gaps. As a result, protons, neutrons, and surviving heavier nuclei are injected into the expanding supernova remnant. We compute the spectra of nuclei escaping from supernova remnants into the interstellar medium, taking into account the observed population of radio pulsars. Our calculations, which include a realistic model for acceleration and propagation of nuclei in pulsar magnetospheres and supernova remnants, predict that heavy nuclei accelerated directly by gamma-ray pulsars could contribute about 20% of the observed cosmic rays in the knee region. Such a contribution of heavy nuclei to the cosmic ray spectrum at the knee can significantly increase the average value of $$ with increasing energy as is suggested by recent observations.Comment: 21 pages, 5 figures, accepted for publication in Astroparticle Physic

On rapid migration and accretion within disks around supermassive black holes

Galactic nuclei should contain a cluster of stars and compact objects in the vicinity of the central supermassive black hole due to stellar evolution, minor mergers and gravitational dynamical friction. By analogy with protoplanetary migration, nuclear cluster objects (NCOs) can migrate in the accretion disks that power active galactic nuclei by exchanging angular momentum with disk gas. Here we show that an individual NCO undergoing runaway outward migration comparable to Type III protoplanetary migration can generate an accretion rate corresponding to Seyfert AGN or quasar luminosities. Multiple migrating NCOs in an AGN disk can dominate traditional viscous disk accretion and at large disk radii, ensemble NCO migration and accretion could provide sufficient heating to prevent the gravitational instability from consuming disk gas in star formation. The magnitude and energy of the X-ray soft excess observed at ~0.1-1keV in Seyfert AGN could be explained by a small population of ~10^{2}-10^{3} accreting stellar mass black holes or a few ULXs. NCO migration and accretion in AGN disks are therefore extremely important mechanisms to add to realistic models of AGN disks.Comment: 6 pages, 2 figures, MNRAS Letters (accepted

Statistical techniques for detecting the intergalactic magnetic field from large samples of extragalactic Faraday rotation data

Rotation measure (RM) grids of extragalactic radio sources have been widely used for studying cosmic magnetism. However, their potential for exploring the intergalactic magnetic field (IGMF) in filaments of galaxies is unclear, since other Faraday-rotation media such as the radio source itself, intervening galaxies, and the interstellar medium of our Galaxy are all significant contributors. We study statistical techniques for discriminating the Faraday rotation of filaments from other sources of Faraday rotation in future large-scale surveys of radio polarization. We consider a 30?? ?? 30?? field of view toward the south Galactic pole, while varying the number of sources detected in both present and future observations. We select sources located at high redshifts and toward which depolarization and optical absorption systems are not observed so as to reduce the RM contributions from the sources and intervening galaxies. It is found that a high-pass filter can satisfactorily reduce the RM contribution from the Galaxy since the angular scale of this component toward high Galactic latitudes would be much larger than that expected for the IGMF. Present observations do not yet provide a sufficient source density to be able to estimate the RM of filaments. However, from the proposed approach with forthcoming surveys, we predict significant residuals of RM that should be ascribable to filaments. The predicted structure of the IGMF down to scales of 0.??1 should be observable with data from the Square Kilometre Array, if we achieve selections of sources toward which sightlines do not contain intervening galaxies and RM errors are less than a few rad m -2.open1

Impact of Hydrogen Bonding on the Susceptibility of Peptides to Oxidation

The tendency of peptides to be oxidized is intimately connected with their function and even their ability to exist in an oxidative environment. Here we report high-level theoretical studies that show that hydrogen bonding can alter the susceptibility of peptides to oxidation, with complexation to a hydrogen-bond acceptor facilitating oxidation, and vice versa, impacting the feasibility of a diverse range of biological processes. It can even provide an energetically viable mechanistic alternative to direct hydrogen-atom abstraction. We find that hydrogen bonding to representative reactive groups leads to a broad (?400?kJ?mol?1) spectrum of ionization energies in the case of model amide, thiol and phenol systems. While some of the oxidative processes at the extreme ends of the spectrum are energetically prohibitive, subtle environmental and solvent effects could potentially mitigate the situation, leading to a balance between hydrogen bonding and oxidative susceptibility

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