Algebraic construction of quantum integrable models including inhomogeneous models

Exploiting the quantum integrability condition we construct an ancestor model associated with a new underlying quadratic algebra. This ancestor model represents an exactly integrable quantum lattice inhomogeneous anisotropic model and at its various realizations and limits can generate a wide range of integrable models. They cover quantum lattice as well as field models associated with the quantum $R$-matrix of trigonometric type or at the undeformed $q \to 1$ limit similar models belonging to the rational class. The classical limit likewise yields the corresponding classical discrete and field models. Thus along with the generation of known integrable models in a unifying way a new class of inhomogeneous models including variable mass sine-Gordon model, inhomogeneous Toda chain, impure spin chains etc. are constructed.Comment: Latex, 14pages, To be published in the Rev. Math. Phys annual conf.ROMP99 Proceedings (Tarun, Poland, 1999

Inflation and nonequilibrium renormalization group

We study de spectrum of primordial fluctuations and the scale dependence of the inflaton spectral index due to self-interactions of the field. We compute the spectrum of fluctuations by applying nonequilibrium renormalization group techniques.Comment: 6 pages, 1 figure, submitted to J. Phys.

Algebraic approach in unifying quantum integrable models

A novel algebra underlying integrable systems is shown to generate and unify a large class of quantum integrable models with given $R$-matrix, through reductions of an ancestor Lax operator and its different realizations. Along with known discrete and field models a new class of inhomogeneous and impurity models are obtained.Comment: Revtex, 6 pages, no figure, revised version to be published in Phys. Rev. Lett., 199

Damping Rates and Mean Free Paths of Soft Fermion Collective Excitations in a Hot Fermion-Gauge-Scalar Theory

We study the transport coefficients, damping rates and mean free paths of soft fermion collective excitations in a hot fermion-gauge-scalar plasma with the goal of understanding the main physical mechanisms that determine transport of chirality in scenarios of non-local electroweak baryogenesis. The focus is on identifying the different transport coefficients for the different branches of soft collective excitations of the fermion spectrum. These branches correspond to collective excitations with opposite ratios of chirality to helicity and different dispersion relations. By combining results from the hard thermal loop (HTL) resummation program with a novel mechanism of fermion damping through heavy scalar decay, we obtain a robust description of the different damping rates and mean free paths for the soft collective excitations to leading order in HTL and lowest order in the Yukawa coupling. The space-time evolution of wave packets of collective excitations unambiguously reveals the respective mean free paths. We find that whereas both the gauge and scalar contribution to the damping rates are different for the different branches, the difference of mean free paths for both branches is mainly determined by the decay of the heavy scalar into a hard fermion and a soft collective excitation. We argue that these mechanisms are robust and are therefore relevant for non-local scenarios of baryogenesis either in the Standard Model or extensions thereof.Comment: REVTeX, 19 pages, 4 eps figures, published versio

Control of star formation by supersonic turbulence

Understanding the formation of stars in galaxies is central to much of modern astrophysics. For several decades it has been thought that stellar birth is primarily controlled by the interplay between gravity and magnetostatic support, modulated by ambipolar diffusion. Recently, however, both observational and numerical work has begun to suggest that support by supersonic turbulence rather than magnetic fields controls star formation. In this review we outline a new theory of star formation relying on the control by turbulence. We demonstrate that although supersonic turbulence can provide global support, it nevertheless produces density enhancements that allow local collapse. Inefficient, isolated star formation is a hallmark of turbulent support, while efficient, clustered star formation occurs in its absence. The consequences of this theory are then explored for both local star formation and galactic scale star formation. (ABSTRACT ABBREVIATED)Comment: Invited review for "Reviews of Modern Physics", 87 pages including 28 figures, in pres

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

Evidence for a “Wattle and Daub” Model of the Cyst Wall of Entamoeba

The cyst wall of Entamoeba invadens (Ei), a model for the human pathogen Entamoeba histolytica, is composed of fibrils of chitin and three chitin-binding lectins called Jacob, Jessie3, and chitinase. Here we show chitin, which was detected with wheat germ agglutinin, is made in secretory vesicles prior to its deposition on the surface of encysting Ei. Jacob lectins, which have tandemly arrayed chitin-binding domains (CBDs), and chitinase, which has an N-terminal CBD, were each made early during encystation. These results are consistent with their hypothesized roles in cross-linking chitin fibrils (Jacob lectins) and remodeling the cyst wall (chitinase). Jessie3 lectins likely form the mortar or daub of the cyst wall, because 1) Jessie lectins were made late during encystation; 2) the addition to Jessie lectins to the cyst wall correlated with a marked decrease in the permeability of cysts to nucleic acid stains (DAPI) and actin-binding heptapeptide (phalloidin); and 3) recombinant Jessie lectins, expressed as a maltose-binding proteins in the periplasm of Escherichia coli, caused transformed bacteria to agglutinate in suspension and form a hard pellet that did not dissociate after centrifugation. Jessie3 appeared as linear forms and rosettes by negative staining of secreted recombinant proteins. These findings provide evidence for a “wattle and daub” model of the Entamoeba cyst wall, where the wattle or sticks (chitin fibrils likely cross-linked by Jacob lectins) is constructed prior to the addition of the mortar or daub (Jessie3 lectins)