Temperature Variation of Ultra Slow Light in a Cold Gas

A model is developed to explain the temperature dependence of the group velocity as observed in the experiments of Hau et al (Nature {\bf397}, 594 (1999)). The group velocity is quite sensitive to the change in the spatial density. The inhomogeneity in the density and its temperature dependence are primarily responsible for the observed behavior.Comment: 12 pages, 4 figure

On Two Models of the Light Pulse Delay in a Saturable Absorber

A comparative analysis of two approaches to description of the light modulation pulse delay in a saturable absorber is presented. According to the simplest model, the delay of the optical pulse is a result of distortion of its shape due to absorption self-modulation in the nonlinear medium. The second model of the effect, proposed at the beginning of our century, connects the pulse delay with the so-called "slow light" resulting from the group velocity reduction under conditions of the coherent population oscillations. It is shown that all the known experimental data on the light pulse delay in saturable absorbers can be comprehensively described in the framework of the simplest model of saturable absorber and do not require invoking the effect of coherent population oscillations with spectral hole-burning and anomalous modifications of the light group velocity. It is concluded that the effect of group velocity reduction under conditions of coherent population oscillations has not received so far any experimental confirmation, and the assertions about real observation of the "slow light" based on this mechanism are groundless.Comment: Regretfully, the journal version of the paper (in Optics and Spectroscopy) appeared to be strongly corrupted due to ignorant editing. In particular, "coherent population oscillations" (CPO) was replaced by "population coherent oscillations" (PCO), "bleaching" - by "clearing", and "bleachable absorber " - by "clearable absorber". Here we present original version of the pape

Vacuum Squeezing in Atomic Media via Self-Rotation

When linearly polarized light propagates through a medium in which elliptically polarized light would undergo self-rotation, squeezed vacuum can appear in the orthogonal polarization. A simple relationship between self-rotation and the degree of vacuum squeezing is developed. Taking into account absorption, we find the optimum conditions for squeezing in any medium that can produce self-rotation. We then find analytic expressions for the amount of vacuum squeezing produced by an atomic vapor when light is near-resonant with a transition between various low-angular-momentum states. Finally, we consider a gas of multi-level Rb atoms, and analyze squeezing for light tuned near the D-lines under realistic conditions.Comment: 10 pages, 6 figures; Submitted to PR

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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

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

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

Propagation dynamics in an autoionization medium

Published versio

Steep optical wave group velocity reduction and storage of light without electromagnetically induced transparency

We report experimental investigationd of optical pulse group velocity reduction and probe pulse regeneration using a Raman scheme. The new scheme which does not rely on the on-one-photon resonance electromagnetically induced transparency (EIT), has many advantages over the conventional method which critically relys on the transparency window created by an EIT process. We demonstrate significant reduction of group velocity, less probe field loss, reduced probe pulse distortion, and high probe pulse regeneration efficiency.Comment: Submitted to Phys. Rev. Lett. on December 21, 2001 (To replace the original submital in which equations were not ip-loaded properly