317 research outputs found
Topological Properties of Spatial Coherence Function
Topology of the spatial coherence function is considered in details. The
phase singularity (coherence vortices) structures of coherence function are
classified by Hopf index and Brouwer degree in topology. The coherence flux
quantization and the linking of the closed coherence vortices are also studied
from the topological properties of the spatial coherence function.Comment: 9 page
Topology of Knotted Optical Vortices
Optical vortices as topological objects exist ubiquitously in nature. In this
paper, by making use of the -mapping topological current theory, we
investigate the topology in the closed and knotted optical vortices. The
topological inner structure of the optical vortices are obtained, and the
linking of the knotted optical vortices is also given.Comment: 11 pages, no figures, accepted by Commun. Theor. Phys. (Beijing, P.
R. China
Knotted Topological Phase Singularities of Electromagnetic Field
In this paper, knotted objects (RS vortices) in the theory of topological
phase singularity in electromagnetic field have been investigated in details.
By using the -mapping topological current theory proposed by Prof. Duan,
we rewrite the topological current form of RS vortices and use this topological
current we reveal that the Hopf invariant of RS vortices is just the sum of the
linking and self-linking numbers of the knotted RS vortices. Furthermore, the
conservation of the Hopf invariant in the splitting, the mergence and the
intersection processes of knotted RS vortices is also discussed.Comment: 6 pages, no figures, author's name have been correcte
Universal switching of plasmonic signals using optical resonator modes
We propose and investigate, both experimentally and theoretically, a novel mechanism for switching and modulating plasmonic
signals based on a Fano interference process, which arises from the coupling between a narrow-band optical Fabry–Pérot cavity
and a surface plasmon polariton (SPP) source. The SPP wave emitted from the cavity is actively modulated in the vicinity of the
cavity resonances by altering the cavity Q-factor and/or resonant frequencies. We experimentally demonstrate dynamic SPP modulation
both by mechanical control of the cavity length and all-optically by harnessing the ultrafast nonlinearity of the Au mirrors
that form the cavity. An electro-optical modulation scheme is also proposed and numerically illustrated. Dynamic operation of
the switch via mechanical means yields a modulation in the SPP coupling efficiency of ~ 80%, while the all-optical control provides
an ultrafast modulation with an efficiency of 30% at a rate of ~ 0.6 THz. The experimental observations are supported by
both analytical and numerical calculations of the mechanical, all-optical and electro-optical modulation methods
Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline
Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds
Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression
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
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