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 inclusive jet cross sections in pp and PbPb collisions at s NN =2.76 TeV

Abstract: Inclusive jet spectra from pp and PbPb collisions at a nucleon-nucleon center-of-mass energy of 2.76TeV, collected with the CMS detector at the CERN Large Hadron Collider, are presented. Jets are reconstructed with three different distance parameters (R=0.2, 0.3, and 0.4) for transverse momentum (pT) greater than 70GeV/c and pseudorapidity |η|<2. Next-to-leading-order quantum chromodynamic calculations with nonperturbative corrections are found to overpredict jet production cross sections in pp for small distance parameters. The jet nuclear modification factors for PbPb compared to pp collisions, show a steady decrease from peripheral to central events, along with a weak dependence on the jet pT. They are found to be independent of the distance parameter in the measured kinematic range.

Constraints on cosmic strings from the ligo-virgo gravitational-wave detectors

Abstract: Cosmic strings can give rise to a large variety of interesting astrophysical phenomena. Among them, powerful bursts of gravitational waves (GWs) produced by cusps are a promising observational signature. In this Letter we present a search for GWs from cosmic string cusps in data collected by the LIGO and Virgo gravitational wave detectors between 2005 and 2010, with over 625 days of live time. We find no evidence of GW signals from cosmic strings. From this result, we derive new constraints on cosmic string parameters, which complement and improve existing limits from previous searches for a stochastic background of GWs from cosmic microwave background measurements and pulsar timing data. In particular, if the size of loops is given by the gravitational backreaction scale, we place upper limits on the string tension Gμ below 10−8 in some regions of the cosmic string parameter space.

Search for gravitational waves from primordial black hole binary coalescences in the galactic halo

Abstract: We use data from the second science run of the LIGO gravitational-wave detectors to search for the gravitational waves from primordial black hole binary coalescence with component masses in the range 0.2–1.0M⊙. The analysis requires a signal to be found in the data from both LIGO observatories, according to a set of coincidence criteria. No inspiral signals were found. Assuming a spherical halo with core radius 5 kpc extending to 50 kpc containing nonspinning black holes with masses in the range 0.2–1.0M⊙, we place an observational upper limit on the rate of primordial black hole coalescence of 63 per year per Milky Way halo (MWH) with 90% confidence.

Measurement of the Underlying Event Activity at the LHC with $s= 7$ TeV and Comparison with $s = 0.9$ TeV

Abstract: A measurement of the underlying activity in scattering processes with a hard scale in the several GeV region is performed in proton-proton collisions at sqrt(s) = 0.9 and 7 TeV, using data collected by the CMS experiment at the LHC. The production of charged particles with pseudorapidity |eta| 0.5 GeV/c is studied in the azimuthal region transverse to that of the leading set of charged particles forming a track-jet. A significant growth of the average multiplicity and scalar-pT sum of the particles in the transverse region is observed with increasing pT of the leading track-jet, followed by a much slower rise above a few GeV/c. For track-jet pT larger than a few GeV/c, the activity in the transverse region is approximately doubled with a centre-of-mass energy increase from 0.9 to 7 TeV. Predictions of several QCD-inspired models as implemented in PYTHIA are compared to the data.

Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV

Abstract: The t t-bar production cross section (sigma[t t-bar]) is measured in proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS experiment, corresponding to an integrated luminosity of 2.3 inverse femtobarns. The measurement is performed in events with two leptons (electrons or muons) in the final state, at least two jets identified as jets originating from b quarks, and the presence of an imbalance in transverse momentum. The measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/- 2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction of the standard model.

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 . . .