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.

Search for gravitational-wave bursts from soft gamma repeaters

Abstract: We present a LIGO search for short-duration gravitational waves (GWs) associated with soft gamma ray repeater (SGR) bursts. This is the first search sensitive to neutron star f modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806-20 and 190 lesser events from SGR 1806-20 and SGR 1900+14. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the model-dependent isotropic GW emission energies (at a nominal distance of 10 kpc) between 3×1045 and 9×1052 erg depending on waveform type, detector antenna factors and noise characteristics at the time of the burst. These upper limits are within the theoretically predicted range of some SGR models.

Sorption of Eu(III) on GMZ bentonite in the absence/presence of humic acid studied by batch and XAFS techniques

Abstract: Bentonite has been extensively studied because of its strong sorption ability and low permeability. In this work, the Na-bentonite from Gaomiaozi County (China) has been characterized by XRD, FTIR and acid-base titration. The sorption of Eu(III) on Na-bentonite in the absence/presence of humic acid (HA) was studied at T = 25 ± 2 °C and in 0.01 mol/L NaClO4 solution. The effects of pH, HA, contact time and initial Eu(III) concentrations were also investigated. The results indicate that the sorption of Eu(III) on Na-bentonite was dependent on pH values. The presence of HA had little effect on Eu(III) sorption at low pH values, but decreased Eu(III) sorption at high pH values. X-ray absorption fine structure spectroscopy (XAFS) was applied to characterize the local structural environment of the adsorbed Eu(III) on bare Na-bentonite and HA-bentonite hybrids. The results indicate that Eu(III) was bound to O atoms at a distance of about 2.39 A at pH 4.15. The results are crucial for the evaluation of the sorption and migration of other trivalent lanthanides and actinides in bentonite as backfill materials.

Measurement of the correlation between flow harmonics of different order in lead-lead collisions at √sNN = 2.76 TeV with the ATLAS detector

Abstract: Correlations between the elliptic or triangular flow coefficients v(m) (m = 2 or 3) and other flow harmonics v(n) (n = 2 to 5) are measured using root S-NN = 2.76 TeV Pb + Pb collision data collected in 2010 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 7 mu b(-1). The v(m)-v(n) correlations aremeasured in midrapidity as a function of centrality, and, for events within the same centrality interval, as a function of event ellipticity or triangularity defined in a forward rapidity region. For events within the same centrality interval, v(3) is found to be anticorrelated with v(2) and this anticorrelation is consistent with similar anticorrelations between the corresponding eccentricities, epsilon(2) and epsilon(3). However, it is observed that v(4) increases strongly with v(2), and v(5) increases strongly with both v(2) and v(3). The trend and strength of the v(m) -v(n) correlations for n = 4 and 5 are found to disagree with epsilon(m)-epsilon(n) correlations predicted by initial-geometry models. Instead, these correlations are found to be consistent with the combined effects of a linear contribution to v(n) and a nonlinear term that is a function of v(2)(2) or of v(2)v(3), as predicted by hydrodynamic models. A simple two-component fit is used to separate these two contributions. The extracted linear and nonlinear contributions to v(4) and v(5) are found to be consistent with previously measured event-plane correlations.

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

Abstract: Motivation N(6)-methyl-adenosine (m(6)A) is the most prevalent mRNA methylation but precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide profiling of m(6)A. We previously developed a peak calling algorithm called exomePeak. However, exomePeak over-simplifies data characteristics and ignores the reads' variances among replicates or reads dependency across a site region. To further improve the performance, new model is needed to address these important issues of MeRIP-seq data. Results We propose a novel, graphical model-based peak calling method, MeTPeak, for transcriptome-wide detection of m(6)A sites from MeRIP-seq data. MeTPeak explicitly models read count of an m(6)A site and introduces a hierarchical layer of Beta variables to capture the variances and a Hidden Markov model to characterize the reads dependency across a site. In addition, we developed a constrained Newton's method and designed a log-barrier function to compute analytically intractable, positively constrained Beta parameters. We applied our algorithm to simulated and real biological datasets and demonstrated significant improvement in detection performance and robustness over exomePeak. Prediction results on publicly available MeRIP-seq datasets are also validated and shown to be able to recapitulate the known patterns of m(6)A, further validating the improved performance of MeTPeak. Availability and implementation The package 'MeTPeak' is implemented in R and C ++, and additional details are available at https://github.com/compgenomics/MeTPeak Contact yufei.huang@utsa.edu or xdchoi@gmail.com Supplementary information Supplementary data are available at Bioinformatics online.

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 . . .