Transverse and Longitudinal Bose-Einstein Correlations

We show how a difference in the correlation length longitudinally and transversely, with respect to the jet axis in e+e- annihilation, arises naturally in a model for Bose-Einstein correlations based on the Lund string model. In genuine three-particle correlations the difference is even more apparent and they provide therefore a good probe for the longitudinal stretching of the string field. The correlation length between pion pairs is found to be rather independent of the pion multiplicity and the kaon content of the final state.Comment: 8 page

The Feynman-Wilson gas and the Lund model

We derive a partition function for the Lund fragmentation model and compare it with that of a classical gas. For a fixed rapidity ``volume'' this partition function corresponds to a multiplicity distribution which is very close to a binomial distribution. We compare our results with the multiplicity distributions obtained from the JETSET Monte Carlo for several scenarios. Firstly, for the fragmentation vertices of the Lund string. Secondly, for the final state particles both with and without decays.Comment: Latex, 21+1 pages, 11 figure

Bose-Einstein and Colour Interference in W-pair Decays

We study effects on the W mass measurements at LEP2 from non-perturbative interference effects in the fully hadronic decay channel. Based on a model for Bose-Einstein interference, which is in agreement with LEP1 data, we argue that there are no Bose-Einstein correlations between bosons coming from the different W's. For small reconnection probabilities we rule out the possible experimental signal of colour interference at LEP2, suggested in previous work. The conclusions from this paper are that the theoretical uncertainties in the W mass determination should be smaller than the experimental statistical error.Comment: 12+1 page

Is there screwiness at the end of the QCD cascades?

We discuss what happens at the end of the QCD cascades. We show that, with just a few reasonable assumptions, the emission of soft gluons is constrained to produce an ordered field in the form of a helix. We describe how to modify the Lund fragmentation scheme in order to fragment such a field. Our modified fragmentation scheme yields results which are consistent with current experimental measurements, but predicts at least one signature which should be observable.Comment: 21+1 page

High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer

Peer reviewe

Metabolomics of Ulva lactuca Linnaeus (Chlorophyta) exposed to oil fuels: Fourier transform infrared spectroscopy and multivariate analysis as tools for metabolic fingerprint

Fossil fuels, e.g. gasoline and diesel oil, account for substantial share of the pollution that affects marine ecosystems. Environmental metabolomics is an emerging field that may help unravel the effect of these xenobiotics on seaweeds and provide methodologies for biomonitoring coastal ecosystems. In the present study, FTIR and multivariate analysis were used to discriminate metabolic profiles of Ulva lactuca after in vitro exposure to diesel oil and gasoline, in combinations of concentrations (0.001%, 0.01%, 0.1%, and 1.0% - v/v) and times of exposure (30 min, 1 h, 12 h, and 24 h). PCA and HCA performed on entire mid-infrared spectral window were able to discriminate diesel oil-exposed thalli from the gasoline-exposed ones. HCA performed on spectral window related to the protein absorbance (17001500 cm 1) enabled the best discrimination between gasoline-exposed samples regarding the time of exposure, and between diesel oil-exposed samples according to the concentration. The results indicate that the combination of FTIR with multivariate analysis is a simple and efficient methodology for metabolic profiling with potential use for biomonitoring strategies.To Coordination for the Improvement of Higher Education Personnel (CAPES) for financial support. The research fellowships granted to Marcelo Maraschin (Proc. 307099/2015-6) and Fernanda Ramlov (Proc. 473408/2013-9) by National Council of Technological and Scientific Development (CNPq) are also acknowledged. This work was partially funded by CNPq and FCT agreement through the PropMine (Proc. 490383/2013-0) and PVE (Proc. 407323/2013-9, Dr. Miguel Rocha) grants

Prioritizing single-nucleotide variations that potentially regulate alternative splicing

Recent evidence suggests that many complex diseases are caused by genetic variations that play regulatory roles in controlling gene expression. Most genetic studies focus on nonsynonymous variations that can alter the amino acid composition of a protein and are therefore believed to have the highest impact on phenotype. Synonymous variations, however, can also play important roles in disease pathogenesis by regulating pre-mRNA processing and translational control. In this study, we systematically survey the effects of single-nucleotide variations (SNVs) on binding affinity of RNA-binding proteins (RBPs). Among the 10,113 synonymous SNVs identified in 697 individuals in the 1,000 Genomes Project and distributed by Genetic Analysis Workshop 17 (GAW17), we identified 182 variations located in alternatively spliced exons that can significantly change the binding affinity of nine RBPs whose binding preferences on 7-mer RNA sequences were previously reported. We found that the minor allele frequencies of these variations are similar to those of nonsynonymous SNVs, suggesting that they are in fact functional. We propose a workflow to identify phenotype-associated regulatory SNVs that might affect alternative splicing from exome-sequencing-derived genetic variations. Based on the affecting SNVs on the quantitative traits simulated in GAW17, we further identified two and four functional SNVs that are predicted to be involved in alternative splicing regulation in traits Q1 and Q2, respectively

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data

Analyzing data obtained from genome-wide gene expression experiments is challenging due to the quantity of variables, the need for multivariate analyses, and the demands of managing large amounts of data. Here we present the R package pcaGoPromoter, which facilitates the interpretation of genome-wide expression data and overcomes the aforementioned problems. In the first step, principal component analysis (PCA) is applied to survey any differences between experiments and possible groupings. The next step is the interpretation of the principal components with respect to both biological function and regulation by predicted transcription factor binding sites. The robustness of the results is evaluated using cross-validation, and illustrative plots of PCA scores and gene ontology terms are available. pcaGoPromoter works with any platform that uses gene symbols or Entrez IDs as probe identifiers. In addition, support for several popular Affymetrix GeneChip platforms is provided. To illustrate the features of the pcaGoPromoter package a serum stimulation experiment was performed and the genome-wide gene expression in the resulting samples was profiled using the Affymetrix Human Genome U133 Plus 2.0 chip. Array data were analyzed using pcaGoPromoter package tools, resulting in a clear separation of the experiments into three groups: controls, serum only and serum with inhibitor. Functional annotation of the axes in the PCA score plot showed the expected serum-promoted biological processes, e.g., cell cycle progression and the predicted involvement of expected transcription factors, including E2F. In addition, unexpected results, e.g., cholesterol synthesis in serum-depleted cells and NF-κB activation in inhibitor treated cells, were noted. In summary, the pcaGoPromoter R package provides a collection of tools for analyzing gene expression data. These tools give an overview of the input data via PCA, functional interpretation by gene ontology terms (biological processes), and an indication of the involvement of possible transcription factors

Dynamic patterning at the pylorus: Formation of an epithelial intestine–stomach boundary in late fetal life

In the adult mouse, distinct morphological and transcriptional differences separate stomach from intestinal epithelium. Remarkably, the epithelial boundary between these two organs is literally one cell thick. This discrete junction is established suddenly and precisely at embryonic day (E) 16.5, by sharpening a previously diffuse intermediate zone. In the present study, we define the dynamic transcriptome of stomach, pylorus, and intestinal tissues between E14.5 and E16.5. We show that establishment of this boundary is concomitant with the induction of over a thousand genes in intestinal epithelium, and these gene products provide intestinal character. Hence, we call this process intestinalization . We identify specific transcription factors (Hnf4Γ, Creb3l3, and Tcfec) and examine signaling pathways (Hedgehog and Wnt) that may play a role in this process. Finally, we define a unique expression domain at the pylorus itself and detect novel pylorus-specific patterns for the transcription factor Gata3 and the secreted protein nephrocan. Developmental Dynamics 238:3205–3217, 2009. © 2009 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64560/1/22134_ftp.pd