389 research outputs found
Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq.
The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use
Confirmation of general relativity on large scales from weak lensing and galaxy velocities
Although general relativity underlies modern cosmology, its applicability on
cosmological length scales has yet to be stringently tested. Such a test has
recently been proposed, using a quantity, EG, that combines measures of
large-scale gravitational lensing, galaxy clustering and structure growth rate.
The combination is insensitive to 'galaxy bias' (the difference between the
clustering of visible galaxies and invisible dark matter) and is thus robust to
the uncertainty in this parameter. Modified theories of gravity generally
predict values of EG different from the general relativistic prediction
because, in these theories, the 'gravitational slip' (the difference between
the two potentials that describe perturbations in the gravitational metric) is
non-zero, which leads to changes in the growth of structure and the strength of
the gravitational lensing effect3. Here we report that EG = 0.39 +/- 0.06 on
length scales of tens of megaparsecs, in agreement with the general
relativistic prediction of EG 0.4. The measured value excludes a
model within the tensor-vector-scalar gravity theory, which modifies both
Newtonian and Einstein gravity. However, the relatively large uncertainty still
permits models within f(R) theory, which is an extension of general relativity.
A fivefold decrease in uncertainty is needed to rule out these models.Comment: Submitted version; 13 pages, 2 figures. Accepted version and
supplementary material are available at:
http://www.nature.com/nature/journal/v464/n7286/full/nature08857.html
An Electron Fixed Target Experiment to Search for a New Vector Boson A' Decaying to e+e-
We describe an experiment to search for a new vector boson A' with weak
coupling alpha' > 6 x 10^{-8} alpha to electrons (alpha=e^2/4pi) in the mass
range 65 MeV < m_A' < 550 MeV. New vector bosons with such small couplings
arise naturally from a small kinetic mixing of the "dark photon" A' with the
photon -- one of the very few ways in which new forces can couple to the
Standard Model -- and have received considerable attention as an explanation of
various dark matter related anomalies. A' bosons are produced by radiation off
an electron beam, and could appear as narrow resonances with small production
cross-section in the trident e+e- spectrum. We summarize the experimental
approach described in a proposal submitted to Jefferson Laboratory's PAC35,
PR-10-009. This experiment, the A' Experiment (APEX), uses the electron beam of
the Continuous Electron Beam Accelerator Facility at Jefferson Laboratory
(CEBAF) at energies of ~1-4 GeV incident on 0.5-10% radiation length Tungsten
wire mesh targets, and measures the resulting e+e- pairs to search for the A'
using the High Resolution Spectrometer and the septum magnet in Hall A. With a
~1 month run, APEX will achieve very good sensitivity because the statistics of
e+e- pairs will be ~10,000 times larger in the explored mass range than any
previous search for the A' boson. These statistics and the excellent mass
resolution of the spectrometers allow sensitivity to alpha'/alpha one to three
orders of magnitude below current limits, in a region of parameter space of
great theoretical and phenomenological interest. Similar experiments could also
be performed at other facilities, such as the Mainz Microtron.Comment: 19 pages, 12 figures, 2 table
Revealing the planar chemistry of two-dimensional heterostructures at the atomic level
Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devicesopen2
The Cosmological Constant
This is a review of the physics and cosmology of the cosmological constant.
Focusing on recent developments, I present a pedagogical overview of cosmology
in the presence of a cosmological constant, observational constraints on its
magnitude, and the physics of a small (and potentially nonzero) vacuum energy.Comment: 50 pages. Submitted to Living Reviews in Relativity
(http://www.livingreviews.org/), December 199
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Inflation and Dark Energy from spectroscopy at z > 2
The expansion of the Universe is understood to have accelerated during two
epochs: in its very first moments during a period of Inflation and much more
recently, at z < 1, when Dark Energy is hypothesized to drive cosmic
acceleration. The undiscovered mechanisms behind these two epochs represent
some of the most important open problems in fundamental physics. The large
cosmological volume at 2 < z < 5, together with the ability to efficiently
target high- galaxies with known techniques, enables large gains in the
study of Inflation and Dark Energy. A future spectroscopic survey can test the
Gaussianity of the initial conditions up to a factor of ~50 better than our
current bounds, crossing the crucial theoretical threshold of
of order unity that separates single field and
multi-field models. Simultaneously, it can measure the fraction of Dark Energy
at the percent level up to , thus serving as an unprecedented test of
the standard model and opening up a tremendous discovery space
f(R) theories
Over the past decade, f(R) theories have been extensively studied as one of
the simplest modifications to General Relativity. In this article we review
various applications of f(R) theories to cosmology and gravity - such as
inflation, dark energy, local gravity constraints, cosmological perturbations,
and spherically symmetric solutions in weak and strong gravitational
backgrounds. We present a number of ways to distinguish those theories from
General Relativity observationally and experimentally. We also discuss the
extension to other modified gravity theories such as Brans-Dicke theory and
Gauss-Bonnet gravity, and address models that can satisfy both cosmological and
local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in
Relativity, Published version, Comments are welcom
The Formation of the First Massive Black Holes
Supermassive black holes (SMBHs) are common in local galactic nuclei, and
SMBHs as massive as several billion solar masses already exist at redshift z=6.
These earliest SMBHs may grow by the combination of radiation-pressure-limited
accretion and mergers of stellar-mass seed BHs, left behind by the first
generation of metal-free stars, or may be formed by more rapid direct collapse
of gas in rare special environments where dense gas can accumulate without
first fragmenting into stars. This chapter offers a review of these two
competing scenarios, as well as some more exotic alternative ideas. It also
briefly discusses how the different models may be distinguished in the future
by observations with JWST, (e)LISA and other instruments.Comment: 47 pages with 306 references; this review is a chapter in "The First
Galaxies - Theoretical Predictions and Observational Clues", Springer
Astrophysics and Space Science Library, Eds. T. Wiklind, V. Bromm & B.
Mobasher, in pres
Gravitational Waves from Gravitational Collapse
Gravitational wave emission from the gravitational collapse of massive stars
has been studied for more than three decades. Current state of the art
numerical investigations of collapse include those that use progenitors with
realistic angular momentum profiles, properly treat microphysics issues,
account for general relativity, and examine non--axisymmetric effects in three
dimensions. Such simulations predict that gravitational waves from various
phenomena associated with gravitational collapse could be detectable with
advanced ground--based and future space--based interferometric observatories.Comment: 68 pages including 13 figures; revised version accepted for
publication in Living Reviews in Relativity (http://www.livingreviews.org
Measurements of B --> D_s^{(*)+} D^{*(*)} Branching Fractions
This article describes improved measurements by CLEO of the and branching fractions, and first evidence
for the decay , where
represents the sum of the , , and
L=1 charm meson states. Also reported is the first
measurement of the polarization in the decay . A partial reconstruction technique, employing only the fully
reconstructed and slow pion from the decay, enhances sensitivity. The observed branching fractions are
, , and , where the first error is statistical,
the second systematic, and the third is due to the uncertainty in the branching fraction. The measured longitudinal
polarization, , is consistent with
the factorization prediction of 54%.Comment: 26 pages (LaTeX), 15 figures. To be submitted to PR
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