Genetic and other factors determining mannose-binding lectin levels in American Indians: the Strong Heart Study

<p>Abstract</p> <p>Background</p> <p>Mannose-binding lectin (MBL) forms an integral part of the innate immune system. Persistent, subclinical infections and chronic inflammatory states are hypothesized to contribute to the pathogenesis of atherosclerosis. MBL gene (<it>MBL2</it>) variants with between 12 to 25% allele frequency in Caucasian and other populations, result in markedly reduced expression of functional protein. Prospective epidemiologic studies, including a nested, case-control study from the present population, have demonstrated the ability of <it>MBL2 </it>genotypes to predict complications of atherosclerosis,. The genetic control of <it>MBL2 </it>expression is complex and genetic background effects in specific populations are largely unknown.</p> <p>Methods</p> <p>The Strong Heart Study is a longitudinal, cohort study of cardiovascular disease among American Indians. A subset of individuals genotyped for the above mentioned case-control study were selected for analysis of circulating MBL levels by double sandwich ELISA method. Mean MBL levels were compared between genotypic groups and multivariate regression was used to determine other independent factors influencing <it>MBL2 </it>expression.</p> <p>Results</p> <p>Our results confirm the effects of variant structural (B, C, and D) and promoter (H and Y) alleles that have been seen in other populations. In addition, MBL levels were found to be positively associated with male gender and hemoglobin A1c levels, but inversely related to triglyceride levels. Correlation was not found between MBL and other markers of inflammation.</p> <p>Conclusion</p> <p>New data is presented concerning the effects of known genetic variants on MBL levels in an American Indian population, as well as the relationship of <it>MBL2 </it>expression to clinical and environmental factors, including inflammatory markers.</p

Some doubts on the validity of the foreground Galactic contribution subtraction from microwave anisotropies

The Galactic foreground contamination in CMBR anisotropies, especially from the dust component, is not easily separable from the cosmological or extragalactic component. In this paper, some doubts will be raised concerning the validity of the methods used to date to remove Galactic dust emission in order to show that none of them achieves its goal. First, I review the recent bibliography on the topic and discuss critically the methods of foreground subtraction: the cross-correlation with templates, analysis assuming the spectral shape of the Galactic components, the "maximum entropy method", "internal linear combination", and "wavelet-based high resolution fitting of internal templates". Second, I analyse the galactic latitude dependence from WMAP data. The frequency dependence is discussed with the data in the available literature. The result is that all methods of subtracting the Galactic contamination are inaccurate. The galactic latitude dependence analysis or the frequency dependence of the anisotropies in the range 50-250 GHz put a constraint on the maximum Galactic contribution in the power spectrum to be less than a ~10% (68% C. L.) for a ~1 degree scale, and possibly higher for larger scales. The origin of most of the signal in the CMBR anisotropies is not Galactic. In any case, the subtraction of the Galaxy is not accurate enough to allow a "precision Cosmology"; other sources of contamination (extragalactic, solar system) are also present.Comment: 24 pages, 1 figure, accepted to be published in J. Astrophys. Ast

ARPES: A probe of electronic correlations

Angle-resolved photoemission spectroscopy (ARPES) is one of the most direct methods of studying the electronic structure of solids. By measuring the kinetic energy and angular distribution of the electrons photoemitted from a sample illuminated with sufficiently high-energy radiation, one can gain information on both the energy and momentum of the electrons propagating inside a material. This is of vital importance in elucidating the connection between electronic, magnetic, and chemical structure of solids, in particular for those complex systems which cannot be appropriately described within the independent-particle picture. Among the various classes of complex systems, of great interest are the transition metal oxides, which have been at the center stage in condensed matter physics for the last four decades. Following a general introduction to the topic, we will lay the theoretical basis needed to understand the pivotal role of ARPES in the study of such systems. After a brief overview on the state-of-the-art capabilities of the technique, we will review some of the most interesting and relevant case studies of the novel physics revealed by ARPES in 3d-, 4d- and 5d-based oxides.Comment: Chapter to appear in "Strongly Correlated Systems: Experimental Techniques", edited by A. Avella and F. Mancini, Springer Series in Solid-State Sciences (2013). A high-resolution version can be found at: http://www.phas.ubc.ca/~quantmat/ARPES/PUBLICATIONS/Reviews/ARPES_Springer.pdf. arXiv admin note: text overlap with arXiv:cond-mat/0307085, arXiv:cond-mat/020850

Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes

Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases

Azimuthal Angle Correlations for Rapidity Separated Hadron Pairs in d+Au Collisions at sqrt(s_NN) = 200 GeV

We report on two-particle azimuthal angle correlations between charged hadrons at forward/backward (deuteron/gold going direction) rapidity and charged hadrons at mid-rapidity in deuteron-gold (d+Au) and proton-proton (p+p) collisions at sqrt(s_NN) = 200 GeV. Jet structures are observed in the correlations which we quantify in terms of the conditional yield and angular width of away side partners. The kinematic region studied here samples partons in the gold nucleus carrying nucleon momentum fraction x~0.1 to x~0.01. Within this range, we find no x dependence of the jet structure in d+Au collisions.Comment: 330 authors, 6 pages text, 4 figures, no tables. 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

Nuclear Modification Factors for Hadrons At Forward and Backward Rapidities in Deuteron-Gold Collisions at sqrt(s_NN) = 200 GeV

We report on charged hadron production in deuteron-gold reactions at sqrt(s_NN) = 200 GeV. Our measurements in the deuteron-direction cover 1.4 < eta < 2.2, referred to as forward rapidity, and in the gold-direction -2.0 < eta < -1.4, referred to as backward rapidity, and a transverse momentum range p_T = 0.5-4.0 GeV/c. We compare the relative yields for different deuteron-gold collision centrality classes. We observe a suppression relative to binary collision scaling at forward rapidity, sensitive to low momentum fraction (x) partons in the gold nucleus, and an enhancement at backward rapidity, sensitive to high momentum fraction partons in the gold nucleus.Comment: 330 authors, 6 pages text, 4 figures, REVTeX4. Published in Physical Review Letters. Minor changes over previous version in response to referee and editor comments, plus updating of references. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are publicly available at http://www.phenix.bnl.gov/papers.htm

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

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

Since the emergence of next-generation sequencing (NGS) technologies, great effort has been put into the development of tools for analysis of the short reads. In parallel, knowledge is increasing regarding biases inherent in these technologies. Here we discuss four different biases we encountered while analyzing various Illumina datasets. These biases are due to both biological and statistical effects that in particular affect comparisons between different genomic regions. Specifically, we encountered biases pertaining to the distributions of nucleotides across sequencing cycles, to mappability, to contamination of pre-mRNA with mRNA, and to non-uniform hydrolysis of RNA. Most of these biases are not specific to one analyzed dataset, but are present across a variety of datasets and within a variety of genomic contexts. Importantly, some of these biases correlated in a highly significant manner with biological features, including transcript length, gene expression levels, conservation levels, and exon-intron architecture, misleadingly increasing the credibility of results due to them. We also demonstrate the relevance of these biases in the context of analyzing an NGS dataset mapping transcriptionally engaged RNA polymerase II (RNAPII) in the context of exon-intron architecture, and show that elimination of these biases is crucial for avoiding erroneous interpretation of the data. Collectively, our results highlight several important pitfalls, challenges and approaches in the analysis of NGS reads

Jet Structure from Dihadron Correlations in d+Au collisions at sqrt(s_NN) = 200 GeV

Dihadron correlations at high transverse momentum in d+Au collisions at sqrt(s_NN) = 200 GeV at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC). From these correlations we extract several structural characteristics of jets; the root-mean-squared (RMS) transverse momentum of fragmenting hadrons with respect to the jet sqrt(), the mean sine-squared angle between the scattered partons , and the number of particles produced within the dijet that are associated with a high-p_T particle (dN/dx_E distributions). We observe that the fragmentation characteristics of jets in d+Au collisions are very similar to those in p+p collisions and that there is also little dependence on the centrality of the d+Au collision. This is consistent with the nuclear medium having little influence on the fragmentation process. Furthermore, there is no statistically significant increase in the value of from p+p to d+Au collisions. This constrains the amount of multiple scattering that partons undergo in the cold nuclear medium before and after a hard-collision.Comment: 330 authors, 30 pages text, RevTeX4, 42 figures, 20 tables. Submitted to Physical Review C. 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

Transverse-energy distributions at midrapidity in pp++pp, dd++Au, and Au++Au collisions at sNN=62.4\sqrt{s_{_{NN}}}=62.4--200~GeV and implications for particle-production models

Measurements of the midrapidity transverse energy distribution, d\Et/d\eta, are presented for $p$$+$$p$, $d$$+$Au, and Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV and additionally for Au$+$Au collisions at $\sqrt{s_{_{NN}}}=62.4$ and 130 GeV. The d\Et/d\eta distributions are first compared with the number of nucleon participants $N_{\rm part}$, number of binary collisions $N_{\rm coll}$, and number of constituent-quark participants $N_{qp}$ calculated from a Glauber model based on the nuclear geometry. For Au$+$Au, \mean{d\Et/d\eta}/N_{\rm part} increases with $N_{\rm part}$, while \mean{d\Et/d\eta}/N_{qp} is approximately constant for all three energies. This indicates that the two component ansatz, $dE_{T}/d\eta \propto (1-x) N_{\rm part}/2 + x N_{\rm coll}$, which has been used to represent $E_T$ distributions, is simply a proxy for $N_{qp}$, and that the $N_{\rm coll}$ term does not represent a hard-scattering component in $E_T$ distributions. The $dE_{T}/d\eta$ distributions of Au$+$Au and $d$$+$Au are then calculated from the measured $p$$+$$p$ $E_T$ distribution using two models that both reproduce the Au$+$Au data. However, while the number-of-constituent-quark-participant model agrees well with the $d$$+$Au data, the additive-quark model does not.Comment: 391 authors, 24 pages, 19 figures, and 15 Tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are publicly available at http://www.phenix.bnl.gov/papers.htm