50 research outputs found
Hydrogen Epoch of Reionization Array (HERA)
The Hydrogen Epoch of Reionization Array (HERA) is a staged experiment to
measure 21 cm emission from the primordial intergalactic medium (IGM)
throughout cosmic reionization (), and to explore earlier epochs of our
Cosmic Dawn (). During these epochs, early stars and black holes
heated and ionized the IGM, introducing fluctuations in 21 cm emission. HERA is
designed to characterize the evolution of the 21 cm power spectrum to constrain
the timing and morphology of reionization, the properties of the first
galaxies, the evolution of large-scale structure, and the early sources of
heating. The full HERA instrument will be a 350-element interferometer in South
Africa consisting of 14-m parabolic dishes observing from 50 to 250 MHz.
Currently, 19 dishes have been deployed on site and the next 18 are under
construction. HERA has been designated as an SKA Precursor instrument.
In this paper, we summarize HERA's scientific context and provide forecasts
for its key science results. After reviewing the current state of the art in
foreground mitigation, we use the delay-spectrum technique to motivate
high-level performance requirements for the HERA instrument. Next, we present
the HERA instrument design, along with the subsystem specifications that ensure
that HERA meets its performance requirements. Finally, we summarize the
schedule and status of the project. We conclude by suggesting that, given the
realities of foreground contamination, current-generation 21 cm instruments are
approaching their sensitivity limits. HERA is designed to bring both the
sensitivity and the precision to deliver its primary science on the basis of
proven foreground filtering techniques, while developing new subtraction
techniques to unlock new capabilities. The result will be a major step toward
realizing the widely recognized scientific potential of 21 cm cosmology.Comment: 26 pages, 24 figures, 2 table
Effect of promoter architecture on the cell-to-cell variability in gene expression
According to recent experimental evidence, the architecture of a promoter,
defined as the number, strength and regulatory role of the operators that
control the promoter, plays a major role in determining the level of
cell-to-cell variability in gene expression. These quantitative experiments
call for a corresponding modeling effort that addresses the question of how
changes in promoter architecture affect noise in gene expression in a
systematic rather than case-by-case fashion. In this article, we make such a
systematic investigation, based on a simple microscopic model of gene
regulation that incorporates stochastic effects. In particular, we show how
operator strength and operator multiplicity affect this variability. We examine
different modes of transcription factor binding to complex promoters
(cooperative, independent, simultaneous) and how each of these affects the
level of variability in transcription product from cell-to-cell. We propose
that direct comparison between in vivo single-cell experiments and theoretical
predictions for the moments of the probability distribution of mRNA number per
cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte
Measuring femoral lesions despite CT metal artefacts: a cadaveric study
Objective Computed tomography is the modality of choice for measuring osteolysis but suffers from metal-induced artefacts obscuring periprosthetic tissues. Previous papers on metal artefact reduction (MAR) show qualitative improvements, but their algorithms have not found acceptance for clinical applications. We investigated to what extent metal artefacts interfere with the segmentation of lesions adjacent to a metal femoral implant and whether metal artefact reduction improves the manual segmentation of such lesions. Materials and methods We manually created 27 periprosthetic lesions in 10 human cadaver femora. We filled the lesions with a fibrotic interface tissue substitute. Each femur was fitted with a polished tapered cobalt-chrome prosthesis and imaged twice—once with the metal, and once with a substitute resin prosthesis inserted. Metalaffected CTs were processed using standard back-projection as well as projection interpolation (PI) MAR. Two experienced users segmented all lesions and compared segmentation accuracy. Results We achieved accurate delineation of periprosthetic lesions in the metal-free images. The presence of a metal implant led us to underestimate lesion volume and introduced geometrical errors in segmentation boundaries.MediamaticsElectrical Engineering, Mathematics and Computer Scienc
Optimizing Sparse RFI Prediction using Deep Learning
Radio Frequency Interference (RFI) is an ever-present limiting factor among
radio telescopes even in the most remote observing locations. When looking to
retain the maximum amount of sensitivity and reduce contamination for Epoch of
Reionization studies, the identification and removal of RFI is especially
important. In addition to improved RFI identification, we must also take into
account computational efficiency of the RFI-Identification algorithm as radio
interferometer arrays such as the Hydrogen Epoch of Reionization Array grow
larger in number of receivers. To address this, we present a Deep Fully
Convolutional Neural Network (DFCN) that is comprehensive in its use of
interferometric data, where both amplitude and phase information are used
jointly for identifying RFI. We train the network using simulated HERA
visibilities containing mock RFI, yielding a known "ground truth" dataset for
evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model
is performed on observations from the 67 dish build-out, HERA-67, and achieves
a data throughput of 1.6 HERA time-ordered 1024 channeled
visibilities per hour per GPU. We determine that relative to an amplitude only
network including visibility phase adds important adjacent time-frequency
context which increases discrimination between RFI and Non-RFI. The inclusion
of phase when predicting achieves a Recall of 0.81, Precision of 0.58, and
score of 0.75 as applied to our HERA-67 observations.Comment: 11 pages, 7 figure
HI 21cm Cosmology and the Bi-spectrum: Closure Diagnostics in Massively Redundant Interferometric Arrays
New massively redundant low frequency arrays allow for a novel investigation
of closure relations in interferometry. We employ commissioning data from the
Hydrogen Epoch of Reionization Array to investigate closure quantities in this
densely packed grid array of 14m antennas operating at 100 MHz to 200 MHz. We
investigate techniques that utilize closure phase spectra for redundant triads
to estimate departures from redundancy for redundant baseline visibilities. We
find a median absolute deviation from redundancy in closure phase across the
observed frequency range of about 4.5deg. This value translates into a
non-redundancy per visibility phase of about 2.6deg, using prototype
electronics. The median absolute deviations from redundancy decrease with
longer baselines. We show that closure phase spectra can be used to identify
ill-behaved antennas in the array, independent of calibration. We investigate
the temporal behavior of closure spectra. The Allan variance increases after a
one minute stride time, due to passage of the sky through the primary beam of
the transit telescope. However, the closure spectra repeat to well within the
noise per measurement at corresponding local sidereal times (LST) from day to
day. In future papers in this series we will develop the technique of using
closure phase spectra in the search for the HI 21cm signal from cosmic
reionization.Comment: 32 pages. 11 figures. Accepted to Radio Scienc
Mitigating Internal Instrument Coupling for 21 cm Cosmology. II. A Method Demonstration with the Hydrogen Epoch of Reionization Array
We present a study of internal reflection and cross-coupling systematics in Phase I of the Hydrogen Epoch of Reionization Array (HERA). In a companion paper, we outlined the mathematical formalism for such systematics and presented algorithms for modeling and removing them from the data. In this work, we apply these techniques to data from HERA's first observing season as a method demonstration. The data show evidence for systematics that, without removal, would hinder a detection of the 21 cm power spectrum for the targeted Epoch of Reionization (EoR) line-of-sight modes in the range 0.2 h −1 Mpc−1 < < 0.5 h −1 Mpc−1. In particular, we find evidence for nonnegligible amounts of spectral structure in the raw autocorrelations that overlaps with the EoR window and is suggestive of complex instrumental effects. Through systematic modeling on a single night of data, we find we can recover these modes in the power spectrum down to the integrated noise floor, achieving a dynamic range in the EoR window of 106 in power (mK2 units) with respect to the bright galactic foreground signal. Future work with deeper integrations will help determine whether these systematics can continue to be mitigated down to EoR levels. For future observing seasons, HERA will have upgraded analog and digital hardware to better control these systematics in the field
Detection of Cosmic Structures using the Bispectrum Phase. II. First Results from Application to Cosmic Reionization Using the Hydrogen Epoch of Reionization Array
Characterizing the epoch of reionization (EoR) at via the
redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern
astrophysics and cosmology, and thus a key science goal of many current and
planned low-frequency radio telescopes. The primary challenge to detecting this
signal is the overwhelmingly bright foreground emission at these frequencies,
placing stringent requirements on the knowledge of the instruments and
inaccuracies in analyses. Results from these experiments have largely been
limited not by thermal sensitivity but by systematics, particularly caused by
the inability to calibrate the instrument to high accuracy. The interferometric
bispectrum phase is immune to antenna-based calibration and errors therein, and
presents an independent alternative to detect the EoR HI fluctuations while
largely avoiding calibration systematics. Here, we provide a demonstration of
this technique on a subset of data from the Hydrogen Epoch of Reionization
Array (HERA) to place approximate constraints on the brightness temperature of
the intergalactic medium (IGM). From this limited data, at we infer
"" upper limits on the IGM brightness temperature to be
"pseudo" mK at "pseudo" Mpc (data-limited)
and "pseudo" mK at "pseudo" Mpc
(noise-limited). The "pseudo" units denote only an approximate and not an exact
correspondence to the actual distance scales and brightness temperatures. By
propagating models in parallel to the data analysis, we confirm that the
dynamic range required to separate the cosmic HI signal from the foregrounds is
similar to that in standard approaches, and the power spectrum of the
bispectrum phase is still data-limited (at dynamic range)
indicating scope for further improvement in sensitivity as the array build-out
continues.Comment: 22 pages, 12 figures (including sub-figures). Published in PhRvD.
Abstract may be slightly abridged compared to the actual manuscript due to
length limitations on arXi
What does an interferometer really measure? Including instrument and data characteristics in the reconstruction of the 21cm power spectrum
Combining the visibilities measured by an interferometer to form a
cosmological power spectrum is a complicated process in which the window
functions play a crucial role. In a delay-based analysis, the mapping between
instrumental space, made of per-baseline delay spectra, and cosmological space
is not a one-to-one relation. Instead, neighbouring modes contribute to the
power measured at one point, with their respective contributions encoded in the
window functions. To better understand the power spectrum measured by an
interferometer, we assess the impact of instrument characteristics and analysis
choices on the estimator by deriving its exact window functions, outside of the
delay approximation. Focusing on HERA as a case study, we find that
observations made with long baselines tend to correspond to enhanced low-k
tails of the window functions, which facilitate foreground leakage outside the
wedge, whilst the choice of bandwidth and frequency taper can help narrow them
down. With the help of simple test cases and more realistic visibility
simulations, we show that, apart from tracing mode mixing, the window functions
can accurately reconstruct the power spectrum estimator of simulated
visibilities. We note that the window functions depend strongly on the
chromaticity of the beam, and less on its spatial structure - a Gaussian
approximation, ignoring side lobes, is sufficient. Finally, we investigate the
potential of asymmetric window functions, down-weighting the contribution of
low-k power to avoid foreground leakage. The window functions presented in this
work correspond to the latest HERA upper limits for the full Phase I data. They
allow an accurate reconstruction of the power spectrum measured by the
instrument and can be used in future analyses to confront theoretical models
and data directly in cylindrical space.Comment: 18 pages, 18 figures, submitted to MNRAS. Comments welcome