Screening of human gene promoter activities using transfected-cell arrays

Promoters are the best characterized transcriptional regulatory sequences in complex genomes because of their predictable location immediately upstream of transcription start sites. Despite a substantial body of literature describing transcriptional promoters, the identification of true start sites for all human transcripts is far from complete. The same is true of the key structural and functional elements responsible for promoter action in different cell types. In order to identify elements responsible for promoter activity, we applied transfected-cell array technology to functionally evaluate promoters for genes involved in inflammatory bowel disease. Seventy-four promoters were examined by reverse transfection of a promoter-fluorescent reporter constructs into a human embryonic kidney cell line (HEK293T). Sixteen (21.6%) promoters were found to be active in HEK293 T cells. Correlations between promoter activity and endogenous transcript level were calculated, and 75% of active promoters were found to be associated with transcriptional activity of their gene counterparts. These results provide experimental evidence of promoter activity, which may aid in understanding the regulation of gene expression. Moreover, this is the first large-scale functional study of regulatory sequences to use a high-throughput transfected-cell array technique

Centrality dependence of charged hadron production in deuteron+gold and nucleon+gold collisions at sqrt(s_NN)=200 GeV

We present transverse momentum (p_T) spectra of charged hadrons measured in deuteron-gold and nucleon-gold collisions at \sqrts = 200 GeV for four centrality classes. Nucleon-gold collisions were selected by tagging events in which a spectator nucleon was observed in one of two forward rapidity detectors. The spectra and yields were investigated as a function of the number of binary nucleon-nucleon collisions, \nu, suffered by deuteron nucleons. A comparison of charged particle yields to those in p+p collisions show that the yield per nucleon-nucleon collision saturates with \nu for high momentum particles. We also present the charged hadron to neutral pion ratios as a function of p_T.Comment: 330 authors, 15 pages text, 16 figures, 3 tables. Submitted to Phys. Rev. Lett. v2 has minor changes to reflect revisions during review process. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

System Size and Energy Dependence of Jet-Induced Hadron Pair Correlation Shapes in Cu+Cu and Au+Au Collisions at sqrt(s_NN) = 200 and 62.4 GeV

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from {dijets} in Cu+Cu and Au+Au collisions at sqrt(s_NN) = 62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from \Delta\phi=\pi in central and semi-central collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.Comment: 464 authors from 60 institutions, 6 pages, 3 figures, 2 tables. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet

Centrality Dependence of pi^0 and eta Production at Large Transverse Momentum in sqrt(s_NN) = 200 GeV d+Au Collisions

The dependence of transverse momentum spectra of neutral pions and eta mesons with p_T <16 GeV/c and p_T < 12 GeV/c, respectively, on the centrality of the collision has been measured at mid-rapidity by the PHENIX experiment at RHIC in d+Au collisions at sqrt(s_(NN)) = 200 GeV. The measured yields are compared to those in p + p collisions at the same sqrt(s_(NN)) scaled by the number of underlying nucleon-nucleon collisions in d+Au. At all centralities the yield ratios show no suppression, in contrast to the strong suppression seen for central Au+Au collisions at RHIC. Only a weak p_T and centrality dependence can be observed.Comment: 332 authors, 6 pages text, 2 figures, one table. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of direct photon production in p + p collisions at sqrt(s) = 200 GeV

Cross sections for mid-rapidity production of direct photons in p+p collisions at the Relativistic Heavy Ion Collider (RHIC) are reported for 3 < p_T < 16 GeV/c. Next-to-leading order (NLO) perturbative QCD (pQCD) describes the data well for p_T > 5 GeV/c, where the uncertainties of the measurement and theory are comparable. We also report on the effect of requiring the photons to be isolated from parton jet energy. The observed fraction of isolated photons is well described by pQCD for p_T > 7 GeV/c.Comment: 330 authors, 6 pages text, 3 figures, one table. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Elliptic flow for phi mesons and (anti)deuterons in Au+Au collisions at sqrt(s_NN) = 200 GeV

Differential elliptic flow (v_2) for phi mesons and (anti)deuterons (d^bar)d is measured for Au+Au collisions at sqrt(s_NN) = 200 GeV. The v_2 for phi mesons follows the trend of lighter pi^+/- and K^+/- mesons, suggesting that ordinary hadrons interacting with standard hadronic cross sections are not the primary driver for elliptic flow development. The v_2 values for (d^bar)d suggest that elliptic flow is additive for composite particles. This further validation of the universal scaling of v_2 per constituent quark for baryons and mesons suggests that partonic collectivity dominates the transverse expansion dynamics.Comment: 343 authors, 6 pages text, 3 figures, REVTeX4. To be submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm