3,535 research outputs found
Influenza Viruses Display High-Affinity Binding to Human Polyglycosylceramides Represented on a Solid-Phase Assay Surface
AbstractPolyglycosylceramides (PGCs), complex glycolipids containing up to 50 or more sugar residues, are recognized as the minor components of the cell-surface membranes, but a knowledge on their tissue distribution, structure, and function is limited. In this study, the binding of influenza viruses to preparations of PGCs was investigated using a TLC overlay assay and a microwell adsorption assay. The ability of PGCs to bind influenza virus was dependent on the source from which they were derived. Preparations of PGCs from human erythrocytes were found to support binding of A and B influenza virus strains at a much lower concentration than sialyl-6-paragloboside and to be somewhat better receptors for these viruses compared to the sialylglycoprotein fetuin. A high virus-binding activity of PGCs suggests that these species could potentially serve as biologically important cell-surface receptors for influenza viruses
Probabilistic quantitative microbial risk assessment model of farmer exposure to Cryptosporidium spp. in irrigation water within Kumasi Metropolis-Ghana
Complementarity and the uncertainty relations
We formulate a general complementarity relation starting from any Hermitian
operator with discrete non-degenerate eigenvalues. We then elucidate the
relationship between quantum complementarity and the Heisenberg-Robertson's
uncertainty relation. We show that they are intimately connected. Finally we
exemplify the general theory with some specific suggested experiments.Comment: 9 pages, 4 figures, REVTeX, uses epsf.sty and multicol.st
A robust sample of galaxies at redshifts 6.0<z<8.7: stellar populations, star-formation rates and stellar masses
We present the results of a photometric redshift analysis designed to
identify z>6 galaxies from the near-IR HST imaging in three deep fields (HUDF,
HUDF09-2 & ERS). By adopting a rigorous set of criteria for rejecting low-z
interlopers, and by employing a deconfusion technique to allow the available
IRAC imaging to be included in the candidate selection process, we have derived
a robust sample of 70 Lyman-break galaxies (LBGs) spanning the redshift range
6.0<z<8.7. Based on our final sample we investigate the distribution of UV
spectral slopes (beta), finding a variance-weighted mean value of =-2.05
+/- 0.09 which, contrary to some previous results, is not significantly bluer
than displayed by lower-redshift starburst galaxies. We confirm the correlation
between UV luminosity and stellar mass reported elsewhere, but based on fitting
galaxy templates featuring a range of star-formation histories, metallicities
and reddening we find that, at z>=6, the range in mass-to-light ratio (M*/L_UV)
at a given UV luminosity could span a factor of ~50. Focusing on a sub-sample
of twenty-one candidates with IRAC detections at 3.6-microns we find that L*
LBGs at z~6.5 have a median stellar mass of M* = (2.1 +/- 1.1) x 10^9 Msun and
a median specific star-formation rate of 1.9 +/- 0.8 Gyr^-1. Using the same
sub-sample we have investigated the influence of nebular continuum and line
emission, finding that for the majority of candidates (16 out of 21) the
best-fitting stellar-mass estimates are reduced by less than a factor of 2.5.
Finally, a detailed comparison of our final sample with the results of previous
studies suggests that, at faint magnitudes, several high-redshift galaxy
samples in the literature are significantly contaminated by low-redshift
interlopers (abridged).Comment: 35 pages, 22 figures, replaced to match version accepted by MNRAS,
minor changes onl
Differential expression analysis for sequence count data
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq
Effects of metal enrichment and metal cooling in galaxy growth and cosmic star formation history
We present the results of a numerical study on the effects of metal
enrichment and metal cooling on galaxy formation and cosmic star formation (SF)
history using cosmological hydrodynamic simulations. We find following
differences in the simulation with metal cooling when compared to the run
without it: (1) the cosmic star formation rate (SFR) is enhanced by about 50 &
20% at z=1 & 3, respectively; (2) the gas mass fraction in galaxies is lower;
(3) the total baryonic mass function (gas + star) at z=3 does not differ
significantly, but shows an increase in the number of relatively massive
galaxies at z=1; (4) the baryonic mass fraction of intergalactic medium (IGM)
is reduced at z<3 due to more efficient cooling and gas accretion onto
galaxies. Our results suggest that the metal cooling enhances the galaxy growth
by two different mechanisms: (1) increase of SF efficiency in the local
interstellar medium (ISM), and (2) increase of IGM accretion onto galaxies. The
former process is effective throughout most of the cosmic history, while the
latter is effective only at z<3 when the IGM is sufficiently enriched by metals
owing to feedback.Comment: 16 pages, 11 figures, 1 table, accepted for publication in MNRAS. A
full resolution version is available at
http://www.physics.unlv.edu/~jhchoi/astro-ph/Metalcooling.pd
The Boundary Conditions of the Heliosphere: Photoionization Models Constrained by Interstellar and In Situ Data
The boundary conditions of the heliosphere are set by the ionization, density
and composition of inflowing interstellar matter. Constraining the properties
of the Local Interstellar Cloud (LIC) at the heliosphere requires radiative
transfer ionization models. We model the background interstellar radiation
field using observed stellar FUV and EUV emission and the diffuse soft X-ray
background. We also model the emission from the boundary between the LIC and
the hot Local Bubble (LB) plasma, assuming that the cloud is evaporating
because of thermal conduction. We create a grid of models covering a plausible
range of LIC and LB properties, and use the modeled radiation field as input to
radiative transfer/thermal equilibrium calculations using the Cloudy code. Data
from in situ observations of He^O, pickup ions and anomalous cosmic rays in the
heliosphere, and absorption line measurements towards epsilon CMa were used to
constrain the input parameters. A restricted range of assumed LIC HI column
densities and LB plasma temperatures produce models that match all the
observational constraints. The relative weakness of the constraints on N(HI)
and T_h contrast with the narrow limits predicted for the H^O and electron
density in the LIC at the Sun, n(H^0) = 0.19 - 0.20 cm^-3, and n(e) = 0.07 +/-
0.01 cm^-3. Derived abundances are mostly typical for low density gas, with
sub-solar Mg, Si and Fe, possibly subsolar O and N, and S about solar; however
C is supersolar. The interstellar gas at the Sun is warm, low density, and
partially ionized, with n(H) = 0.23 - 0.27 cm^-3, T = 6300 K, X(H^+) ~ 0.2, and
X(He^+) ~ 0.4. These results appear to be robust since acceptable models are
found for substantially different input radiation fields. Our results favor low
values for the reference solar abundances for the LIC composition.Comment: 14 pages, 4 figures, submitted to Astronomy & Astrophysics together
with papers from the International Space Sciences Institute workshop on
Interstellar Hydrogen in the Heliospher
Early star-forming galaxies and the reionization of the Universe
Star forming galaxies represent a valuable tracer of cosmic history. Recent
observational progress with Hubble Space Telescope has led to the discovery and
study of the earliest-known galaxies corresponding to a period when the
Universe was only ~800 million years old. Intense ultraviolet radiation from
these early galaxies probably induced a major event in cosmic history: the
reionization of intergalactic hydrogen. New techniques are being developed to
understand the properties of these most distant galaxies and determine their
influence on the evolution of the universe.Comment: Review article appearing in Nature. This posting reflects a submitted
version of the review formatted by the authors, in accordance with Nature
publication policies. For the official, published version of the review,
please see http://www.nature.com/nature/archive/index.htm
Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage
The informational content of RNA sequencing is currently far from being completely explored. Most of the analyses focus on processing tables of counts or finding isoform deconvolution via exon junctions. This article presents a comparison of several techniques that can be used to estimate differential expression of exons or small genomic regions of expression, based on their coverage function shapes. The problem is defined as finding the differentially expressed exons between two samples using local expression profile normalization and statistical measures to spot the differences between two profile shapes. Initial experiments have been done using synthetic data, and real data modified with synthetically created differential patterns. Then, 160 pipelines (5 types of generator × 4 normalizations × 8 difference measures) are compared. As a result, the best analysis pipelines are selected based on linearity of the differential expression estimation and the area under the ROC curve. These platform-independent techniques have been implemented in the Bioconductor package rnaSeqMap. They point out the exons with differential expression or internal splicing, even if the counts of reads may not show this. The areas of application include significant difference searches, splicing identification algorithms and finding suitable regions for QPCR primers
- …