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.

Einstein@Home search for periodic gravitational waves in LIGO S4 data

Abstract: A search for periodic gravitational waves, from sources such as isolated rapidly spinning neutron stars, was carried out using 510 h of data from the fourth LIGO science run (S4). The search was for quasimonochromatic waves in the frequency range from 50 to 1500 Hz, with a linear frequency drift f˙ (measured at the solar system barycenter) in the range -f/τ

Practical speed meter designs for quantum nondemolition gravitational-wave interferometers

Abstract: In the quest to develop viable designs for third-generation optical interferometric gravitational-wave detectors (e.g., LIGO-III and EURO), one strategy is to monitor the relative momentum or speed of the test-mass mirrors, rather than monitoring their relative position. A previous paper analyzed a straightforward but impractical design for a speed-meter interferometer that accomplishes this. This paper describes some practical variants of speed-meter interferometers. Like the original interferometric speed meter, these designs in principle can beat the gravitational-wave standard quantum limit (SQL) by an arbitrarily large amount, over an arbitrarily wide range of frequencies. These variants essentially consist of a Michelson interferometer plus an extra ``sloshing'' cavity that sends the signal back into the interferometer with opposite phase shift, thereby cancelling the position information and leaving a net phase shift proportional to the relative velocity. In practice, the sensitivity of these variants will be limited by the maximum light power W-circ circulating in the arm cavities that the mirrors can support and by the leakage of vacuum into the optical train at dissipation points. In the absence of dissipation and with squeezed vacuum (power squeeze factor e(-2R)similar or equal to0.1) inserted into the output port so as to keep the circulating power down, the SQL can be beat by h/h(SQL)similar torootW(circ)(SQL)e(-2R)/W-circ at all frequencies below some chosen f(opt)similar or equal to100 Hz. Here W(circ)(SQL)similar or equal to800 kW(f(opt)/100 Hz)(3) is the power required to reach the SQL in the absence of squeezing. (However, as the power increases in this expression, the speed meter becomes more narrow band; additional power and reoptimization of some parameters are required to maintain the wide band. See Sec. III B.) Estimates are given of the amount by which vacuum leakage at dissipation points will debilitate this sensitivity (see Fig. 12); these losses are 10% or less over most of the frequency range of interest (fgreater than or similar to10 Hz). The sensitivity can be improved, particularly at high freqencies, by using frequency-dependent homodyne detection, which unfortunately requires two 4-km-long filter cavities (see Fig. 4).

Reconstruction and identification of τ lepton decays to hadrons and ντ at CMS

Abstract: This paper describes the algorithms used by the CMS experiment to reconstruct and identify tau to hadrons + tau neutrino decays during Run 1 of the LHC. The performance of the algorithms is studied in proton-proton collisions recorded at a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 inverse femtobarns. The algorithms achieve an identification efficiency of 50-60%, with misidentification rates for quark and gluon jets, electrons, and muons between per mille and per cent levels.

Directional Limits on Persistent Gravitational Waves from Advanced LIGO’s First Observing Run

Abstract: We employ gravitational-wave radiometry to map the stochastic gravitational wave background expected from a variety of contributing mechanisms and test the assumption of isotropy using data from the Advanced Laser Interferometer Gravitational Wave Observatory's (aLIGO) first observing run. We also search for persistent gravitational waves from point sources with only minimal assumptions over the 20-1726 Hz frequency band. Finding no evidence of gravitational waves from either point sources or a stochastic background, we set limits at 90% confidence. For broadband point sources, we report upper limits on the gravitational wave energy flux per unit frequency in the range F_{α,Θ}(f)<(0.1-56)×10^{-8} erg cm^{-2} s^{-1} Hz^{-1}(f/25 Hz)^{α-1} depending on the sky location Θ and the spectral power index α. For extended sources, we report upper limits on the fractional gravitational wave energy density required to close the Universe of Ω(f,Θ)<(0.39-7.6)×10^{-8} sr^{-1}(f/25 Hz)^{α} depending on Θ and α. Directed searches for narrowband gravitational waves from astrophysically interesting objects (Scorpius X-1, Supernova 1987 A, and the Galactic Center) yield median frequency-dependent limits on strain amplitude of h_{0}<(6.7,5.5, and 7.0)×10^{-25}, respectively, at the most sensitive detector frequencies between 130-175 Hz. This represents a mean improvement of a factor of 2 across the band compared to previous searches of this kind for these sky locations, considering the different quantities of strain constrained in each case.

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

Abstract: Rice is a major food staple for the world’s population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGIRIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).

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 . . .