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.

First Searches for Optical Counterparts to Gravitational-wave Candidate Events

Abstract: During the Laser Interferometer Gravitational-wave Observatory and Virgo joint science runs in 2009-2010, gravitational wave (GW) data from three interferometer detectors were analyzed within minutes to select GW candidate events and infer their apparent sky positions. Target coordinates were transmitted to several telescopes for follow-up observations aimed at the detection of an associated optical transient. Images were obtained for eight such GW candidates. We present the methods used to analyze the image data as well as the transient search results. No optical transient was identified with a convincing association with any of these candidates, and none of the GW triggers showed strong evidence for being astrophysical in nature. We compare the sensitivities of these observations to several model light curves from possible sources of interest, and discuss prospects for future joint GW-optical observations of this type.

Search for pair-produced vectorlike B quarks in proton-proton collisions at √s = 8 TeV

Abstract: A search for the production of a heavy B quark, having electric charge −1/3 and vector couplings to W, Z, and H bosons, is carried out using proton-proton collision data recorded at the CERN LHC by the CMS experiment, corresponding to an integrated luminosity of 19.7 fb^(−1). The B quark is assumed to be pair produced and to decay in one of three ways: to tW, bZ, or bH. The search is carried out in final states with one, two, and more than two charged leptons, as well as in fully hadronic final states. Each of the channels in the exclusive final-state topologies is designed to be sensitive to specific combinations of the B quark-antiquark pair decays. The observed event yields are found to be consistent with the standard model expectations in all the final states studied. A statistical combination of these results is performed, and upper limits are set on the cross section of the strongly produced B quark-antiquark pairs as a function of the B quark mass. Lower limits on the B quark mass between 740 and 900 GeV are set at a 95% confidence level, depending on the values of the branching fractions of the B quark to tW, bZ, and bH. Overall, these limits are the most stringent to date.

Search for two Higgs bosons in final states containing two photons and two bottom quarks in proton-proton collisions at 8 TeV

Abstract: A search is presented for the production of two Higgs bosons in final states containing two photons and two bottom quarks. Both resonant and nonresonant hypotheses are investigated. The analyzed data correspond to an integrated luminosity of 19.7 fb^(−1) of proton-proton collisions at √s = 8 TeV collected with the CMS detector. Good agreement is observed between data and predictions of the standard model (SM). Upper limits are set at 95% confidence level on the production cross section of new particles and compared to the prediction for the existence of a warped extra dimension. When the decay to two Higgs bosons is kinematically allowed, assuming a mass scale Λ_R = 1 TeV for the model, the data exclude a radion scalar at masses below 980 GeV. The first Kaluza-Klein excitation mode of the graviton in the RS1 Randall-Sundrum model is excluded for masses between 325 and 450 GeV. An upper limit of 0.71 pb is set on the nonresonant two-Higgs-boson cross section in the SM-like hypothesis. Limits are also derived on nonresonant production assuming anomalous Higgs-boson couplings.

Search for charged Higgs bosons from top quark decays in pp̄ collisions at s=1.96TeV

Abstract: We report the results of a search for a charged Higgs boson in the decays of top quarks produced in pp collisions at a center-of-mass energy of 1.96 TeV. We use a data sample corresponding to an integrated luminosity of 193 pb{sup -1} collected by the upgraded Collider Detector at Fermilab. No evidence for charged Higgs production is found, allowing 95% C.L. upper limits to be placed on BR(t{yields}H{sup +}b) for different charged Higgs decay scenarios. In addition, we present in the minimal supersymmetric standard model (m{sub H{sup {+-}}},tan{beta}) plane the first exclusion regions with radiative and Yukawa coupling corrections.

Oligomannurarate sulfate, a novel heparanase inhibitor simultaneously targeting basic fibroblast growth factor, combats tumor angiogenesis and metastasis

Abstract: Inhibitors of tumor angiogenesis and metastasis are increasingly emerging as promising agents for cancer therapy. Recently, heparanase inhibitors have offered a new avenue for such work because heparanase is thought to be critically involved in the metastatic and angiogenic potentials of tumor cells. Here, we report that oligomannurarate sulfate (JG3), a novel marine-derived oligosaccharide, acts as a heparanase inhibitor. Our results revealed that JG3 significantly inhibited tumor angiogenesis and metastasis, both in vitro and in vivo, by combating heparanase activity via binding to the KKDC and QPLK domains of the heparanase molecule. The JG3-heparanase interaction was competitively inhibited by low molecular weight heparin (4,000 Da) but not by other glycosaminoglycans. In addition, JG3 abolished heparanase-driven invasion, inhibited the release of heparan sulfate-sequestered basic fibroblast growth factor (bFGF) from the extracellular matrix, and repressed subsequent angiogenesis. Moreover, JG3 inactivated bFGF-induced bFGF receptor and extracellular signal-regulated kinase 1/2 phosphorylation and blocked bFGF-triggered angiogenic events by directly binding to bFGF. Thus, JG3 seems to inhibit both major heparanase activities by simultaneously acting as a substrate mimetic and as a competitive inhibitor of heparan sulfate. These findings suggest that JG3 should be considered as a promising candidate agent for cancer therapy.

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 . . .