Yi Chen

Bio: Yi Chen is an academic researcher from Chinese Academy of Sciences. The author has contributed to research in topics: Large Hadron Collider & Medicine. The author has an hindex of 217, co-authored 4342 publications receiving 293080 citations. Previous affiliations of Yi Chen include Rochester Institute of Technology & National Institutes of Health.

Measurement of the production cross section of jets in association with a Z boson in pp collisions at √s = 7 TeV with the ATLAS detector

Abstract: Measurements of the production of jets of particles in association with a Z boson in pp collisions at root s = 7 TeV are presented, using data corresponding to an integrated luminosity of 4.6 fb(-1) collected by the ATLAS experiment at the Large Hadron Collider. Inclusive and differential jet cross sections in Z events, with Z decaying into electron or muon pairs, are measured for jets with transverse momentum p(T) > 30 GeV and rapidity vertical bar y vertical bar < 4.4. The results are compared to next-to-leading-order perturbative QCD calculations, and to predictions from different Monte Carlo generators based on leading-order and next-to-leading-order matrix elements supplemented by parton showers.

Improved upper limits on the stochastic gravitational-wave background from 2009-2010 LIGO and Virgo data

Abstract: Gravitational waves from a variety of sources are predicted to superpose to create a stochastic background. This background is expected to contain unique information from throughout the history of the universe that is unavailable through standard electromagnetic observations, making its study of fundamental importance to understanding the evolution of the universe. We carry out a search for the stochastic background with the latest data from LIGO and Virgo. Consistent with predictions from most stochastic gravitational-wave background models, the data display no evidence of a stochastic gravitational-wave signal. Assuming a gravitational-wave spectrum of Omega_GW(f)=Omega_alpha*(f/f_ref)^alpha, we place 95% confidence level upper limits on the energy density of the background in each of four frequency bands spanning 41.5-1726 Hz. In the frequency band of 41.5-169.25 Hz for a spectral index of alpha=0, we constrain the energy density of the stochastic background to be Omega_GW(f)<5.6x10^-6. For the 600-1000 Hz band, Omega_GW(f)<0.14*(f/900 Hz)^3, a factor of 2.5 lower than the best previously reported upper limits. We find Omega_GW(f)<1.8x10^-4 using a spectral index of zero for 170-600 Hz and Omega_GW(f)<1.0*(f/1300 Hz)^3 for 1000-1726 Hz, bands in which no previous direct limits have been placed. The limits in these four bands are the lowest direct measurements to date on the stochastic background. We discuss the implications of these results in light of the recent claim by the BICEP2 experiment of the detection of inflationary gravitational waves.

Study of Z boson production in PbPb collisions at √s NN=2.76TeV

Abstract: A search for Z bosons in the mu^+mu^- decay channel has been performed in PbPb collisions at a nucleon-nucleon centre of mass energy = 2.76 TeV with the CMS detector at the LHC, in a 7.2 inverse microbarn data sample. The number of opposite-sign muon pairs observed in the 60--120 GeV/c^2 invariant mass range is 39, corresponding to a yield per unit of rapidity (y) and per minimum bias event of (33.8 +/- 5.5 (stat) +/- 4.4 (syst)) 10^{-8}, in the |y|<2.0 range. Rapidity, transverse momentum, and centrality dependencies are also measured. The results agree with next-to-leading order QCD calculations, scaled by the number of incoherent nucleon-nucleon collisions.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

KEGG: Kyoto Encyclopedia of Genes and Genomes

Abstract: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).

limma powers differential expression analyses for RNA-sequencing and microarray studies

Abstract: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

Atherosclerosis — An Inflammatory Disease

Abstract: Atherosclerosis is an inflammatory disease. Because high plasma concentrations of cholesterol, in particular those of low-density lipoprotein (LDL) cholesterol, are one of the principal risk factors for atherosclerosis,1 the process of atherogenesis has been considered by many to consist largely of the accumulation of lipids within the artery wall; however, it is much more than that. Despite changes in lifestyle and the use of new pharmacologic approaches to lower plasma cholesterol concentrations,2,3 cardiovascular disease continues to be the principal cause of death in the United States, Europe, and much of Asia.4,5 In fact, the lesions of atherosclerosis represent . . .