17,809 research outputs found
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments
In many biochemical processes, proteins bound to DNA at distant sites are
brought into close proximity by loops in the underlying DNA. For example, the
function of some gene-regulatory proteins depends on such DNA looping
interactions. We present a new technique for characterizing the kinetics of
loop formation in vitro, as observed using the tethered particle method, and
apply it to experimental data on looping induced by lambda repressor. Our
method uses a modified (diffusive) hidden Markov analysis that directly
incorporates the Brownian motion of the observed tethered bead. We compare
looping lifetimes found with our method (which we find are consistent over a
range of sampling frequencies) to those obtained via the traditional
threshold-crossing analysis (which can vary depending on how the raw data are
filtered in the time domain). Our method does not involve any time filtering
and can detect sudden changes in looping behavior. For example, we show how our
method can identify transitions between long-lived, kinetically distinct states
that would otherwise be difficult to discern
Assumptions of the primordial spectrum and cosmological parameter estimation
The observables of the perturbed universe, CMB anisotropy and large
structures, depend on a set of cosmological parameters, as well as, the assumed
nature of primordial perturbations. In particular, the shape of the primordial
power spectrum (PPS) is, at best, a well motivated assumption. It is known that
the assumed functional form of the PPS in cosmological parameter estimation can
affect the best fit parameters and their relative confidence limits. In this
paper, we demonstrate that a specific assumed form actually drives the best fit
parameters into distinct basins of likelihood in the space of cosmological
parameters where the likelihood resists improvement via modifications to the
PPS. The regions where considerably better likelihoods are obtained allowing
free form PPS lie outside these basins. In the absence of a preferred model of
inflation, this raises a concern that current cosmological parameters estimates
are strongly prejudiced by the assumed form of PPS. Our results strongly
motivate approaches toward simultaneous estimation of the cosmological
parameters and the shape of the primordial spectrum from upcoming cosmological
data. It is equally important for theorists to keep an open mind towards early
universe scenarios that produce features in the PPS.Comment: 11 pages, 2 figures, discussions extended, main results unchanged,
matches published versio
The impact of new signals on precise marine navigation - initial results from an experiment in Harwich Harbour
The General Lighthouse Authorities of the United Kingdom and IrelandĀ (GLAs) are supporting a project at University College London (UCL) to study whether it is possible to meet the International Maritime Organisationās (IMO)Ā future requirements for port and harbour approach using future GNSS constellations, as detailed in IMO resolution A.915. This paper presents the results of a trial focusing on the accuracy, integrity, availability and continuity of port navigation, port approach, and docking. Abstract The required accuracy for docking is 0.1 m (95\%), which currently necessitates the use of Real Time Kinematic (RTK) processing. We consider the single-epoch geometry-based approach, which is robust against loss of lock and will fully benefit from the additional satellites. The trial was held at the beginning of May 2008 and saw THV Alert navigate into Harwich Harbour while satellite observation data were recorded from the vessel and from shore-based reference stations. Additional data were obtained from nearby Ordnance Survey reference stations, and two total stations were used to track the vesselās passage to provide a truth model. Several modernised GPS satellites were tracked. The data were processed under different scenarios, using software developed at UCL, and the positioning performance analysed. Abstract Providing integrity for single-epoch RTK is particularly difficult. The identification of phase observation outliers is not possible before the integer ambiguities are resolved, but an undetected outlier could prevent successful ambiguity resolution. However, it will not always be necessary to fix every ambiguity to achieve the required precision, particularly with a multi-GNSS constellation. This paper introduces a new algorithm for partial ambiguity resolution in the presence of measurement bias that has been developed and tested at UCL.Ā This algorithmĀ results in an improved ambiguity resolution success rate at the expense of computation time
Clustering Via Nonparametric Density Estimation: the R Package pdfCluster
The R package pdfCluster performs cluster analysis based on a nonparametric
estimate of the density of the observed variables. After summarizing the main
aspects of the methodology, we describe the features and the usage of the
package, and finally illustrate its working with the aid of two datasets
The APOGEE-2 Survey of the Orion Star Forming Complex: I. Target Selection and Validation with early observations
The Orion Star Forming Complex (OSFC) is a central target for the APOGEE-2
Young Cluster Survey. Existing membership catalogs span limited portions of the
OSFC, reflecting the difficulty of selecting targets homogeneously across this
extended, highly structured region. We have used data from wide field
photometric surveys to produce a less biased parent sample of young stellar
objects (YSOs) with infrared (IR) excesses indicative of warm circumstellar
material or photometric variability at optical wavelengths across the full 420
square degrees extent of the OSFC. When restricted to YSO candidates with H <
12.4, to ensure S/N ~100 for a six visit source, this uniformly selected sample
includes 1307 IR excess sources selected using criteria vetted by Koenig &
Liesawitz and 990 optical variables identified in the Pan-STARRS1 3
survey: 319 sources exhibit both optical variability and evidence of
circumstellar disks through IR excess. Objects from this uniformly selected
sample received the highest priority for targeting, but required fewer than
half of the fibers on each APOGEE-2 plate. We fill the remaining fibers with
previously confirmed and new color-magnitude selected candidate OSFC members.
Radial velocity measurements from APOGEE-1 and new APOGEE-2 observations taken
in the survey's first year indicate that ~90% of the uniformly selected targets
have radial velocities consistent with Orion membership.The APOGEE-2 Orion
survey will include >1100 bona fide YSOs whose uniform selection function will
provide a robust sample for comparative analyses of the stellar populations and
properties across all sub-regions of Orion.Comment: Accepted for publication in ApJ
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