651 research outputs found
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells
Embryonic stem cells (ESC) have the potential to self-renew indefinitely and
to differentiate into any of the three germ layers. The molecular mechanisms
for self-renewal, maintenance of pluripotency and lineage specification are
poorly understood, but recent results point to a key role for epigenetic
mechanisms. In this study, we focus on quantifying the impact of histone 3
acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We
analyze genome-wide histone acetylation patterns and gene expression profiles
measured over the first five days of cell differentiation triggered by
silencing Nanog, a key transcription factor in ESC regulation. We explore the
temporal and spatial dynamics of histone acetylation data and its correlation
with gene expression using supervised and unsupervised statistical models. On a
genome-wide scale, changes in acetylation are significantly correlated to
changes in mRNA expression and, surprisingly, this coherence increases over
time. We quantify the predictive power of histone acetylation for gene
expression changes in a balanced cross-validation procedure. In an in-depth
study we focus on genes central to the regulatory network of Mouse ESC,
including those identified in a recent genome-wide RNAi screen and in the
PluriNet, a computationally derived stem cell signature. We find that compared
to the rest of the genome, ESC-specific genes show significantly more
acetylation signal and a much stronger decrease in acetylation over time, which
is often not reflected in an concordant expression change. These results shed
light on the complexity of the relationship between histone acetylation and
gene expression and are a step forward to dissect the multilayer regulatory
mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog
An NLO QCD analysis of inclusive cross-section and jet-production data from the ZEUS experiment
The ZEUS inclusive differential cross-section data from HERA, for charged and
neutral current processes taken with e+ and e- beams, together with
differential cross-section data on inclusive jet production in e+ p scattering
and dijet production in \gamma p scattering, have been used in a new NLO QCD
analysis to extract the parton distribution functions of the proton. The input
of jet data constrains the gluon and allows an accurate extraction of
\alpha_s(M_Z) at NLO;
\alpha_s(M_Z) = 0.1183 \pm 0.0028(exp.) \pm 0.0008(model)
An additional uncertainty from the choice of scales is estimated as \pm
0.005. This is the first extraction of \alpha_s(M_Z) from HERA data alone.Comment: 37 pages, 14 figures, to be submitted to EPJC. PDFs available at
http://durpdg.dur.ac.uk/hepdata in LHAPDFv
Precise measurement of the W-boson mass with the CDF II detector
We have measured the W-boson mass MW using data corresponding to 2.2/fb of
integrated luminosity collected in proton-antiproton collisions at 1.96 TeV
with the CDF II detector at the Fermilab Tevatron collider. Samples consisting
of 470126 W->enu candidates and 624708 W->munu candidates yield the measurement
MW = 80387 +- 12 (stat) +- 15 (syst) = 80387 +- 19 MeV. This is the most
precise measurement of the W-boson mass to date and significantly exceeds the
precision of all previous measurements combined
High-E_T dijet photoproduction at HERA
The cross section for high-E_T dijet production in photoproduction has been
measured with the ZEUS detector at HERA using an integrated luminosity of 81.8
pb-1. The events were required to have a virtuality of the incoming photon,
Q^2, of less than 1 GeV^2 and a photon-proton centre-of-mass energy in the
range 142 < W < 293 GeV. Events were selected if at least two jets satisfied
the transverse-energy requirements of E_T(jet1) > 20 GeV and E_T(jet2) > 15 GeV
and pseudorapidity requirements of -1 < eta(jet1,2) < 3, with at least one of
the jets satisfying -1 < eta(jet) < 2.5. The measurements show sensitivity to
the parton distributions in the photon and proton and effects beyond
next-to-leading order in QCD. Hence these data can be used to constrain further
the parton densities in the proton and photon.Comment: 36 pages, 13 figures, 20 tables, including minor revisions from
referees. Accepted by Phys. Rev.
Inclusive jet cross sections and dijet correlations in photoproduction at HERA
Inclusive jet cross sections in photoproduction for events containing a
meson have been measured with the ZEUS detector at HERA using an integrated
luminosity of . The events were required to have a
virtuality of the incoming photon, , of less than 1 GeV, and a
photon-proton centre-of-mass energy in the range . The measurements are compared with next-to-leading-order (NLO) QCD
calculations. Good agreement is found with the NLO calculations over most of
the measured kinematic region. Requiring a second jet in the event allowed a
more detailed comparison with QCD calculations. The measured dijet cross
sections are also compared to Monte Carlo (MC) models which incorporate
leading-order matrix elements followed by parton showers and hadronisation. The
NLO QCD predictions are in general agreement with the data although differences
have been isolated to regions where contributions from higher orders are
expected to be significant. The MC models give a better description than the
NLO predictions of the shape of the measured cross sections.Comment: 43 pages, 12 figures, charm jets ZEU
Search for a narrow charmed baryonic state decaying to D^*+/- p^-/+ in ep collisions at HERA
A resonance search has been made in the D^*+/- p^-/+ invariant-mass spectrum
with the ZEUS detector at HERA using an integrated luminosity of 126 pb^-1. The
decay channels D^*+ -> D^0 pi^+_s -> (K^- pi^+) pi^+_s and D^*+ -> D^0 pi^+_s
-> (K^- pi^+ pi^+ pi^-) pi^+_s (and the corresponding antiparticle decays) were
used to identify D^*+/- mesons. No resonance structure was observed in the
D^*+/- p^-/+ mass spectrum from more than 60000 reconstructed D^*+/- mesons.
The results are not compatible with a report of the H1 Collaboration of a
charmed pentaquark, Theta^0_c.Comment: 22 pages, 7 figures, 1 table; minor text revisions; 2 references
adde
Dissociation of virtual photons in events with a leading proton at HERA
The ZEUS detector has been used to study dissociation of virtual photons in
events with a leading proton, gamma^* p -> X p, in e^+p collisions at HERA. The
data cover photon virtualities in two ranges, 0.03<Q^2<0.60 GeV^2 and 2<Q^2<100
GeV^2, with M_X>1.5 GeV, where M_X is the mass of the hadronic final state, X.
Events were required to have a leading proton, detected in the ZEUS leading
proton spectrometer, carrying at least 90% of the incoming proton energy. The
cross section is presented as a function of t, the squared four-momentum
transfer at the proton vertex, Phi, the azimuthal angle between the positron
scattering plane and the proton scattering plane, and Q^2. The data are
presented in terms of the diffractive structure function, F_2^D(3). A
next-to-leading-order QCD fit to the higher-Q^2 data set and to previously
published diffractive charm production data is presented
Measurement of (anti)deuteron and (anti)proton production in DIS at HERA
The first observation of (anti)deuterons in deep inelastic scattering at HERA
has been made with the ZEUS detector at a centre-of-mass energy of 300--318 GeV
using an integrated luminosity of 120 pb-1. The measurement was performed in
the central rapidity region for transverse momentum per unit of mass in the
range 0.3<p_T/M<0.7. The particle rates have been extracted and interpreted in
terms of the coalescence model. The (anti)deuteron production yield is smaller
than the (anti)proton yield by approximately three orders of magnitude,
consistent with the world measurements.Comment: 26 pages, 9 figures, 5 tables, submitted to Nucl. Phys.
Performance of the CMS Cathode Strip Chambers with Cosmic Rays
The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device
in the CMS endcaps. Their performance has been evaluated using data taken
during a cosmic ray run in fall 2008. Measured noise levels are low, with the
number of noisy channels well below 1%. Coordinate resolution was measured for
all types of chambers, and fall in the range 47 microns to 243 microns. The
efficiencies for local charged track triggers, for hit and for segments
reconstruction were measured, and are above 99%. The timing resolution per
layer is approximately 5 ns
X-ray emission from the Sombrero galaxy: discrete sources
We present a study of discrete X-ray sources in and around the
bulge-dominated, massive Sa galaxy, Sombrero (M104), based on new and archival
Chandra observations with a total exposure of ~200 ks. With a detection limit
of L_X = 1E37 erg/s and a field of view covering a galactocentric radius of ~30
kpc (11.5 arcminute), 383 sources are detected. Cross-correlation with Spitler
et al.'s catalogue of Sombrero globular clusters (GCs) identified from HST/ACS
observations reveals 41 X-rays sources in GCs, presumably low-mass X-ray
binaries (LMXBs). We quantify the differential luminosity functions (LFs) for
both the detected GC and field LMXBs, whose power-low indices (~1.1 for the
GC-LF and ~1.6 for field-LF) are consistent with previous studies for
elliptical galaxies. With precise sky positions of the GCs without a detected
X-ray source, we further quantify, through a fluctuation analysis, the GC LF at
fainter luminosities down to 1E35 erg/s. The derived index rules out a
faint-end slope flatter than 1.1 at a 2 sigma significance, contrary to recent
findings in several elliptical galaxies and the bulge of M31. On the other
hand, the 2-6 keV unresolved emission places a tight constraint on the field
LF, implying a flattened index of ~1.0 below 1E37 erg/s. We also detect 101
sources in the halo of Sombrero. The presence of these sources cannot be
interpreted as galactic LMXBs whose spatial distribution empirically follows
the starlight. Their number is also higher than the expected number of cosmic
AGNs (52+/-11 [1 sigma]) whose surface density is constrained by deep X-ray
surveys. We suggest that either the cosmic X-ray background is unusually high
in the direction of Sombrero, or a distinct population of X-ray sources is
present in the halo of Sombrero.Comment: 11 figures, 5 tables, ApJ in pres
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