177 research outputs found
Electron and Photon Scattering on Three-Nucleon Bound States
A big spectrum of processes induced by real and virtual photons on the 3He
and 3H nuclei is theoretically investigated through many examples based on
nonrelativistic Faddeev calculations for bound and continuum states. The modern
nucleon-nucleon potential AV18 together with the three-nucleon force UrbanaIX
is used. The single nucleon current is augmented by explicit pi- and rho-like
two-body currents which fulfill the current continuity equation together with
the corresponding parts of the AV18 potential. We also employ the Siegert
theorem, which induces many-body contributions to the current operator. The
interplay of these different dynamical ingredients in the various
electromagnetic processes is studied and the theory is compared to the
experimental data. Overall we find fair to good agreement but also cases of
strong disagreement between theory and experiment, which calls for improved
dynamics. In several cases we refer the reader to the work of other groups and
compare their results with ours. In addition we list a number of predictions
for observables in different processes which would challenge this dynamical
scenario even more stringently and systematically.Comment: 154 pages, 80 figures includes as ps files, 21 additional figures as
jpeg file
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
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
Reception Test of Petals for the End Cap TEC+ of the CMS Silicon Strip Tracker
The silicon strip tracker of the CMS experiment has been completed and was inserted into the CMS detector in late 2007. The largest sub system of the tracker are its end caps, comprising two large end caps (TEC) each containing 3200 silicon strip modules. To ease construction, the end caps feature a modular design: groups of about 20 silicon modules are placed on sub-assemblies called petals and these self-contained elements are then mounted onto the TEC support structures. Each end cap consists of 144 such petals, which were built and fully qualified by several institutes across Europe. Fro
Integration of the End Cap TEC+ of the CMS Silicon Strip Tracker
The silicon strip tracker of the CMS experiment has been completed and inserted into the CMS detector in late 2007. The largest sub-system of the tracker is its end cap system, comprising two large end caps (TEC) each containing 3200 silicon strip modules. To ease construction, the end caps feature a modular design: groups of about 20 silicon modules are placed on sub-assemblies called petals and these self-contained elements are then mounted into the TEC support structures. Each end cap consists of 144 petals, and the insertion of these petals into the end cap structure is referred to as TEC integration. The two end caps were integrated independently in Aachen (TEC+) and at CERN (TEC--). This note deals with the integration of TEC+, describing procedures for end cap integration and for quality control during testing of integrated sections of the end cap and presenting results from the testing
How Past and Present Influence the Foraging of Clonal Plants?
Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment
Physics with the KLOE-2 experiment at the upgraded DANE
Investigation at a --factory can shed light on several debated issues
in particle physics. We discuss: i) recent theoretical development and
experimental progress in kaon physics relevant for the Standard Model tests in
the flavor sector, ii) the sensitivity we can reach in probing CPT and Quantum
Mechanics from time evolution of entangled kaon states, iii) the interest for
improving on the present measurements of non-leptonic and radiative decays of
kaons and eta/eta mesons, iv) the contribution to understand the
nature of light scalar mesons, and v) the opportunity to search for narrow
di-lepton resonances suggested by recent models proposing a hidden dark-matter
sector. We also report on the physics in the continuum with the
measurements of (multi)hadronic cross sections and the study of gamma gamma
processes.Comment: 60 pages, 41 figures; added affiliation for one of the authors; added
reference to section
Light Meson Spectroscopy
We survey the current status of light meson spectroscopy. We begin with a
general introduction to meson spectroscopy and and its importance in
understanding the physical states of Quantum Chromo Dynamics (QCD).
Phemenological models of hadron spectroscopy are described with particular
emphasis on the constituent quark model and the qualitative features it
predicts for the meson spectrum. We next discuss expectations for hadrons lying
outside the quark model, such as hadron states with excited gluonic degrees of
freedom. These states include so-called hybrids glueballs}, as well as
multiquark states. The established meson states are compared to the quark model
predictions and we find that most meson states are well described by the quark
model. However, a number of states in the light-quark sector do not fit in
well, suggesting the existence of hadronic states with additional degrees of
freedom. We end with a brief description of future directions in meson
spectroscopy.Comment: 111 pages with 28 imbedded figures, in LaTeX2e with no special
macros. Submitted to Reviews of Modern Physics, Nov.12, 199
- …