Tunable Modulational Instability Sidebands via Parametric Resonance in Periodically Tapered Optical Fibers

We analyze the modulation instability induced by periodic variations of group velocity dispersion and nonlinearity in optical fibers, which may be interpreted as an analogue of the well-known parametric resonance in mechanics. We derive accurate analytical estimates of resonant detuning, maximum gain and instability margins, significantly improving on previous literature on the subject. We also design a periodically tapered photonic crystal fiber, in order to achieve narrow instability sidebands at a detuning of 35 THz, above the Raman maximum gain peak of fused silica. The wide tunability of the resonant peaks by variations of the tapering period and depth will allow to implement sources of correlated photon pairs which are far-detuned from the input pump wavelength, with important applications in quantum optics.Comment: 15 pages, 7 figure

A multiwavelength study on the high-energy behaviour of Fermi/LAT pulsars

Using archival as well as freshly acquired data, we assess the X-ray behaviour of the Fermi/LAT gamma-ray pulsars listed in the First Fermi source catalog. After revisiting the relationships between the pulsars' rotational energy losses and their X and gamma-ray luminosities, we focus on the distance-indipendent gamma to X-ray flux ratios. When plotting our Fgamma/Fx values as a function of the pulsars' rotational energy losses, one immediately sees that pulsars with similar energetics have Fgamma/Fx spanning 3 decades. Such spread, most probably stemming from vastly different geometrical configurations of the X and gamma-ray emitting regions, defies any straightforward interpretation of the plot. Indeed, while energetic pulsars do have low Fgamma/Fx values, little can be said for the bulk of the Fermi neutron stars. Dividing our pulsar sample into radio-loud and radio-quiet subsamples, we find that, on average, radio-quiet pulsars do have higher values of Fgamma/Fx, implying an intrinsec faintness of their X-ray emission and/or a different geometrical configuration. Moreover, despite the large spread mentioned above, statistical tests show a lower scatter in the radio-quiet dataset with respect to the radio-loud one, pointing to a somewhat more constrained geometry for the radio-quiet objects with respect to the radio-loud ones.Comment: 39 pages, 5 figures, 3 tables. To be published in Astrophysical Journa

Cosmic rays in the surroundings of SNR G35.6-0.4

HESS J1858+020 is a TeV gamma-ray source that was reported not to have any clear cataloged counterpart at any wavelength. However, it has been recently proposed that this source is indirectly associated with the radio source, re-identified as a supernova remnant (SNR), G35.6-0.4. The latter is found to be middle-aged ($\sim 30$ kyr) and to have nearby molecular clouds (MCs). HESS J1858+020 was proposed to be the result of the interaction of protons accelerated in the SNR shell with target ions residing in the clouds. The Fermi Large Area Telescope (LAT) First Source Catalog does not list any source coincident with the position of HESS J1858+020, but some lie close. Here, we analyse more than 2 years of data obtained with the Fermi-LAT for the region of interest, and consider whether it is indeed possible that the closest LAT source, 1FGL J1857.1+0212c, is related to HESS J1858+020. We conclude it is not, and we impose upper limits on the GeV emission originating from HESS J1858+020. Using a simplified 3D model for the cosmic-ray propagation out from the shell of the SNR, we consider whether the interaction between SNR G35.6-0.4 and the MCs nearby could give rise to the TeV emission of HESS J1858+020 without producing a GeV counterpart. If so, the pair of SNR/TeV source with no GeV detection would be reminiscent of other similarly-aged SNRs, such as some of the TeV hotspots near W28, for which cosmic-ray diffusion may be used to explain their multi-frequency phenomenology. However, for HESS J1858+020, we found that although the phase space in principle allows for such GeV--TeV non-correlation to appear, usual and/or observationally constrained values of the parameters (e.g., diffusion coefficients and cloud-SNR likely distances) would disfavor it.Comment: In press in MNRA

The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNA

BACKGROUND Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector. RESULTS We performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3'UTR of protein coding genes. Unusually, many TEs and the 3'UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs. CONCLUSIONS This is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements

Dominance of Orientation over Frequency in the Perception of 3-D Slant and Shape

In images of textured three-dimensional surfaces, pattern changes can be characterized as changes in orientation and spatial frequency, features for which neurons in primary visual cortex are classically selective. Previously, we have demonstrated that correct 3-D shape perception is contingent on the visibility of orientation flows that run parallel to the surface curvature. We sought to determine the relative contributions of orientation modulations (OMs) and frequency modulations (FMs) for the detection of slant and shape from 3-D surfaces. Results show that 1) when OM and FM indicate inconsistent degrees of surface slant or curvature, observer responses were consistent with the slant or curvature specified by OM even if the FM indicated a slant or curvature in the opposite direction to the same degree. 2) For slanted surfaces, OM information dictates slant perception at both shallow and steep slants while FM information is effective only for steep slants. Together these results point to a dominant role of OM information in the perception of 3-D slant and shape

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