1,685 research outputs found
High-Throughput SNP Genotyping by SBE/SBH
Despite much progress over the past decade, current Single Nucleotide
Polymorphism (SNP) genotyping technologies still offer an insufficient degree
of multiplexing when required to handle user-selected sets of SNPs. In this
paper we propose a new genotyping assay architecture combining multiplexed
solution-phase single-base extension (SBE) reactions with sequencing by
hybridization (SBH) using universal DNA arrays such as all -mer arrays. In
addition to PCR amplification of genomic DNA, SNP genotyping using SBE/SBH
assays involves the following steps: (1) Synthesizing primers complementing the
genomic sequence immediately preceding SNPs of interest; (2) Hybridizing these
primers with the genomic DNA; (3) Extending each primer by a single base using
polymerase enzyme and dideoxynucleotides labeled with 4 different fluorescent
dyes; and finally (4) Hybridizing extended primers to a universal DNA array and
determining the identity of the bases that extend each primer by hybridization
pattern analysis. Our contributions include a study of multiplexing algorithms
for SBE/SBH genotyping assays and preliminary experimental results showing the
achievable tradeoffs between the number of array probes and primer length on
one hand and the number of SNPs that can be assayed simultaneously on the
other. Simulation results on datasets both randomly generated and extracted
from the NCBI dbSNP database suggest that the SBE/SBH architecture provides a
flexible and cost-effective alternative to genotyping assays currently used in
the industry, enabling genotyping of up to hundreds of thousands of
user-specified SNPs per assay.Comment: 19 page
COrE (Cosmic Origins Explorer) A White Paper
COrE (Cosmic Origins Explorer) is a fourth-generation full-sky,
microwave-band satellite recently proposed to ESA within Cosmic Vision
2015-2025. COrE will provide maps of the microwave sky in polarization and
temperature in 15 frequency bands, ranging from 45 GHz to 795 GHz, with an
angular resolution ranging from 23 arcmin (45 GHz) and 1.3 arcmin (795 GHz) and
sensitivities roughly 10 to 30 times better than PLANCK (depending on the
frequency channel). The COrE mission will lead to breakthrough science in a
wide range of areas, ranging from primordial cosmology to galactic and
extragalactic science. COrE is designed to detect the primordial gravitational
waves generated during the epoch of cosmic inflation at more than
for . It will also measure the CMB gravitational lensing
deflection power spectrum to the cosmic variance limit on all linear scales,
allowing us to probe absolute neutrino masses better than laboratory
experiments and down to plausible values suggested by the neutrino oscillation
data. COrE will also search for primordial non-Gaussianity with significant
improvements over Planck in its ability to constrain the shape (and amplitude)
of non-Gaussianity. In the areas of galactic and extragalactic science, in its
highest frequency channels COrE will provide maps of the galactic polarized
dust emission allowing us to map the galactic magnetic field in areas of
diffuse emission not otherwise accessible to probe the initial conditions for
star formation. COrE will also map the galactic synchrotron emission thirty
times better than PLANCK. This White Paper reviews the COrE science program,
our simulations on foreground subtraction, and the proposed instrumental
configuration.Comment: 90 pages Latex 15 figures (revised 28 April 2011, references added,
minor errors corrected
Combinatorics and Geometry of Transportation Polytopes: An Update
A transportation polytope consists of all multidimensional arrays or tables
of non-negative real numbers that satisfy certain sum conditions on subsets of
the entries. They arise naturally in optimization and statistics, and also have
interest for discrete mathematics because permutation matrices, latin squares,
and magic squares appear naturally as lattice points of these polytopes.
In this paper we survey advances on the understanding of the combinatorics
and geometry of these polyhedra and include some recent unpublished results on
the diameter of graphs of these polytopes. In particular, this is a thirty-year
update on the status of a list of open questions last visited in the 1984 book
by Yemelichev, Kovalev and Kravtsov and the 1986 survey paper of Vlach.Comment: 35 pages, 13 figure
Inflation and the Scale Dependent Spectral Index: Prospects and Strategies
We consider the running of the spectral index as a probe of both inflation
itself, and of the overall evolution of the very early universe. Surveying a
collection of simple single field inflationary models, we confirm that the
magnitude of the running is relatively consistent, unlike the tensor amplitude,
which varies by orders of magnitude. Given this target, we confirm that the
running is potentially detectable by future large scale structure or 21 cm
observations, but that only the most futuristic measurements can distinguish
between these models on the basis of their running. For any specified
inflationary scenario, the combination of the running index and unknown
post-inflationary expansion history induces a theoretical uncertainty in the
predicted value of the spectral index. This effect can easily dominate the
statistical uncertainty with which Planck and its successors are expected to
measure the spectral index. More positively, upcoming cosmological experiments
thus provide an intriguing probe of physics between TeV and GUT scales by
constraining the reheating history associated with any specified inflationary
model, opening a window into the "primordial dark age" that follows the end of
inflation.Comment: 32 pages. v2 and v3 Minor reference updates /clarification
Delay Differential Analysis of Seizures in Multichannel Electrocorticography Data
High-density electrocorticogram (ECoG) electrodes are capable of recording neurophysiological data with high temporal resolution with wide spatial coverage. These recordings are a window to understanding how the human brain processes information and subsequently behaves in healthy and pathologic states. Here, we describe and implement delay differential analysis (DDA) for the characterization of ECoG data obtained from human patients with intractable epilepsy. DDA is a time-domain analysis framework based on embedding theory in nonlinear dynamics that reveals the nonlinear invariant properties of an unknown dynamical system. The DDA embedding serves as a low-dimensional nonlinear dynamical basis onto which the data are mapped. This greatly reduces the risk of overfitting and improves the method's ability to fit classes of data. Since the basis is built on the dynamical structure of the data, preprocessing of the data (e.g., filtering) is not necessary. We performed a large-scale search for a DDA model that best fit ECoG recordings using a genetic algorithm to qualitatively discriminate between different cortical states and epileptic events for a set of 13 patients. A single DDA model with only three polynomial terms was identified. Singular value decomposition across the feature space of the model revealed both global and local dynamics that could differentiate electrographic and electroclinical seizures and provided insights into highly localized seizure onsets and diffuse seizure terminations. Other common ECoG features such as interictal periods, artifacts, and exogenous stimuli were also analyzed with DDA. This novel framework for signal processing of seizure information demonstrates an ability to reveal unique characteristics of the underlying dynamics of the seizure and may be useful in better understanding, detecting, and maybe even predicting seizures
Supersymmetry at the Tevatron ?
These lectures contain an introduction to the search for supersymmetry at
hadron colliders. The Tevatron is one of high-energy physics most sophisticated
tools. The high center-of-mass energy of its proton-antiproton collisions makes
it an ideal place to search for physics beyond the Standard Model, such as
supersymmetry. Two experiments, CDF and D\O, completed a long data taking
period in summer of 1995, yielding over of proton-- antiproton
interactions. The data recorded by the experiments are still being analysed.
The lectures outline the strategies in the search for supersymmetry at the
Tevatron and examine the major analyses in detail. Results obtained by the two
experiments are included where available.Comment: 40 pages, 13 figure
CMB-S4 Science Book, First Edition
This book lays out the scientific goals to be addressed by the
next-generation ground-based cosmic microwave background experiment, CMB-S4,
envisioned to consist of dedicated telescopes at the South Pole, the high
Chilean Atacama plateau and possibly a northern hemisphere site, all equipped
with new superconducting cameras. CMB-S4 will dramatically advance cosmological
studies by crossing critical thresholds in the search for the B-mode
polarization signature of primordial gravitational waves, in the determination
of the number and masses of the neutrinos, in the search for evidence of new
light relics, in constraining the nature of dark energy, and in testing general
relativity on large scales
Parton theory of magnetic polarons: Mesonic resonances and signatures in dynamics
When a mobile hole is moving in an anti-ferromagnet it distorts the
surrounding Neel order and forms a magnetic polaron. Such interplay between
hole motion and anti-ferromagnetism is believed to be at the heart of high-Tc
superconductivity in cuprates. We study a single hole described by the t-Jz
model with Ising interactions between the spins in 2D. This situation can be
experimentally realized in quantum gas microscopes. When the hole hopping is
much larger than couplings between the spins, we find strong evidence that
magnetic polarons can be understood as bound states of two partons, a spinon
and a holon carrying spin and charge quantum numbers respectively. We introduce
a microscopic parton description which is benchmarked by comparison with
results from advanced numerical simulations. Using this parton theory, we
predict a series of excited states that are invisible in the spectral function
and correspond to rotational excitations of the spinon-holon pair. This is
reminiscent of mesonic resonances observed in high-energy physics, which can be
understood as rotating quark antiquark pairs. We also apply the strong coupling
parton theory to study far-from equilibrium dynamics of magnetic polarons
observable in current experiments with ultracold atoms. Our work supports
earlier ideas that partons in a confining phase of matter represent a useful
paradigm in condensed-matter physics and in the context of high-Tc
superconductivity. While direct observations of spinons and holons in real
space are impossible in traditional solid-state experiments, quantum gas
microscopes provide a new experimental toolbox. We show that, using this
platform, direct observations of partons in and out-of equilibrium are
possible. Extensions of our approach to the t-J model are also discussed. Our
predictions in this case are relevant to current experiments with quantum gas
microscopes for ultracold atoms.Comment: 30 pages, 4 appendices, 26 figure
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