973 research outputs found
SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicing Fingerprints
Splicing event identification is one of the most important issues in the comprehensive analysis of transcription profile. Recent development of next-generation sequencing technology has generated an extensive profile of alternative splicing. However, while many of these splicing events are between exons that are relatively close on genome sequences, reads generated by RNA-Seq are not limited to alternative splicing between close exons but occur in virtually all splicing events. In this work, a novel method, SAW, was proposed for the identification of all splicing events based on short reads from RNA-Seq. It was observed that short reads not in known gene models are actually absent words from known gene sequences. An efficient method to filter and cluster these short reads by fingerprint fragments of splicing events without aligning short reads to genome sequences was developed. Additionally, the possible splicing sites were also determined without alignment against genome sequences. A consensus sequence was then generated for each short read cluster, which was then aligned to the genome sequences. Results demonstrated that this method could identify more than 90% of the known splicing events with a very low false discovery rate, as well as accurately identify, a number of novel splicing events between distant exons
Flavor Mediation Delivers Natural SUSY
If supersymmetry (SUSY) solves the hierarchy problem, then naturalness
considerations coupled with recent LHC bounds require non-trivial superpartner
flavor structures. Such "Natural SUSY" models exhibit a large mass hierarchy
between scalars of the third and first two generations as well as degeneracy
(or alignment) among the first two generations. In this work, we show how this
specific beyond the standard model (SM) flavor structure can be tied directly
to SM flavor via "Flavor Mediation". The SM contains an anomaly-free SU(3)
flavor symmetry, broken only by Yukawa couplings. By gauging this flavor
symmetry in addition to SM gauge symmetries, we can mediate SUSY breaking via
(Higgsed) gauge mediation. This automatically delivers a natural SUSY spectrum.
Third-generation scalar masses are suppressed due to the dominant breaking of
the flavor gauge symmetry in the top direction. More subtly, the
first-two-generation scalars remain highly degenerate due to a custodial U(2)
symmetry, where the SU(2) factor arises because SU(3) is rank two. This
custodial symmetry is broken only at order (m_c/m_t)^2. SUSY gauge coupling
unification predictions are preserved, since no new charged matter is
introduced, the SM gauge structure is unaltered, and the flavor symmetry treats
all matter multiplets equally. Moreover, the uniqueness of the anomaly-free
SU(3) flavor group makes possible a number of concrete predictions for the
superpartner spectrum.Comment: 17 pages, 7 figures, 2 tables. v2 references added, minor changes to
flavor constraints and a little discussion adde
Bayesian Fit of Exclusive Decays: The Standard Model Operator Basis
We perform a model-independent fit of the short-distance couplings
within the Standard Model set of and operators. Our analysis of , and decays is the first to harness the full
power of the Bayesian approach: all major sources of theory uncertainty
explicitly enter as nuisance parameters. Exploiting the latest measurements,
the fit reveals a flipped-sign solution in addition to a Standard-Model-like
solution for the couplings . Each solution contains about half of the
posterior probability, and both have nearly equal goodness of fit. The Standard
Model prediction is close to the best-fit point. No New Physics contributions
are necessary to describe the current data. Benefitting from the improved
posterior knowledge of the nuisance parameters, we predict ranges for currently
unmeasured, optimized observables in the angular distributions of .Comment: 42 pages, 8 figures; v2: Using new lattice input for f_Bs,
considering Bs-mixing effects in BR[B_s->ll]. Main results and conclusion
unchanged, matches journal versio
A fourth generation, anomalous like-sign dimuon charge asymmetry and the LHC
A fourth chiral generation, with in the range GeV and a moderate value of the CP-violating phase can explain the
anomalous like-sign dimuon charge asymmetry observed recently by the D0
collaboration. The required parameters are found to be consistent with
constraints from other and decays. The presence of such quarks, apart
from being detectable in the early stages of the LHC, would also have important
consequences in the electroweak symmetry breaking sector.Comment: 18 pages, 9 figures, Figure 1 is modified, more discussions are added
in section 2. new references adde
Dynamical Boson Stars
The idea of stable, localized bundles of energy has strong appeal as a model
for particles. In the 1950s John Wheeler envisioned such bundles as smooth
configurations of electromagnetic energy that he called {\em geons}, but none
were found. Instead, particle-like solutions were found in the late 1960s with
the addition of a scalar field, and these were given the name {\em boson
stars}. Since then, boson stars find use in a wide variety of models as sources
of dark matter, as black hole mimickers, in simple models of binary systems,
and as a tool in finding black holes in higher dimensions with only a single
killing vector. We discuss important varieties of boson stars, their dynamic
properties, and some of their uses, concentrating on recent efforts.Comment: 79 pages, 25 figures, invited review for Living Reviews in
Relativity; major revision in 201
Search for rare quark-annihilation decays, B --> Ds(*) Phi
We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context
of the Standard Model, these decays are expected to be highly suppressed since
they proceed through annihilation of the b and u-bar quarks in the B- meson.
Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected
with the BABAR detector at SLAC. We find no evidence for these decays, and we
set Bayesian 90% confidence level upper limits on the branching fractions BF(B-
--> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results
are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid
Communications
Diffractive Dijet Production at sqrt(s)=630 and 1800 GeV at the Fermilab Tevatron
We report a measurement of the diffractive structure function of
the antiproton obtained from a study of dijet events produced in association
with a leading antiproton in collisions at GeV at the
Fermilab Tevatron. The ratio of at GeV to
obtained from a similar measurement at GeV is compared with
expectations from QCD factorization and with theoretical predictions. We also
report a measurement of the (-Pomeron) and ( of parton in
Pomeron) dependence of at GeV. In the region
, GeV and , is
found to be of the form , which obeys
- factorization.Comment: LaTeX, 9 pages, Submitted to Phys. Rev. Letter
A Study of B0 -> J/psi K(*)0 pi+ pi- Decays with the Collider Detector at Fermilab
We report a study of the decays B0 -> J/psi K(*)0 pi+ pi-, which involve the
creation of a u u-bar or d d-bar quark pair in addition to a b-bar -> c-bar(c
s-bar) decay. The data sample consists of 110 1/pb of p p-bar collisions at
sqrt{s} = 1.8 TeV collected by the CDF detector at the Fermilab Tevatron
collider during 1992-1995. We measure the branching ratios to be BR(B0 -> J/psi
K*0 pi+ pi-) = (8.0 +- 2.2 +- 1.5) * 10^{-4} and BR(B0 -> J/psi K0 pi+ pi-) =
(1.1 +- 0.4 +- 0.2) * 10^{-3}. Contributions to these decays are seen from
psi(2S) K(*)0, J/psi K0 rho0, J/psi K*+ pi-, and J/psi K1(1270)
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
Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS
The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured
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