1,037 research outputs found
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
High transverse momentum eta meson production in p+p, d+Au and Au+Au collisions at sqrt(s_NN) = 200 GeV
Inclusive transverse momentum spectra of eta mesons in the range p_T~2-12
GeV/c have been measured at mid-rapidity (|\eta| < 0,35) by the PHENIX
experiment at RHIC in p+p, d+Au and Au+Au collisions at sqrt(s_NN) = 200 GeV.
The eta mesons are reconstructed through their eta--> \gamma\gamma channel for
the three colliding systems as well as through the eta-->pi^0 pi+ pi- decay
mode in p+p and d+Au collisions. The nuclear modification factor in d+Au
collisions, R_dAu(p_T~1.0-1.1, suggests at most only modest p_T broadening
("Cronin enhancement"). In central Au+Au reactions, the eta yields are
significantly suppressed, with R_AuAu(pT)~0.2. The ratio of eta to pi^0 yields
is approximately constant as a function of p_T for the three colliding systems
in agreement with the high-p_T world average of R_eta/pi^0 \approx 0.5 in
hadron-hadron, hadron-nucleus, and nucleus-nucleus collisions for a wide range
of center-of-mass energies [sqrt(s_NN)~3-1800 GeV] as well as, for high scaled
momentum x_p, in e+e- annihilations at sqrt(s)=91.2 GeV. These results are
consistent with a scenario where high-p_T eta production in nuclear collisions
at RHIC is largely unaffected by initial-state effects, but where light-quark
mesons (pi^0;eta) are equally suppressed due to final-state interactions of the
parent partons in the dense medium produced in Au+Au reactions.Comment: 391 authors, NN pages text, RevTeX4, figures, 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
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