51 research outputs found
A Computational Clonal Analysis of the Developing Mouse Limb Bud
A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study tissue movement during morphogenesis. Such experiments allow cell populations to be labeled at an early stage of development and to follow their spatial evolution over time. However, disentangling the cumulative effects of the multiple events responsible for the expansion of the labeled cell population is not always straightforward. To overcome this problem, we develop a novel computational method that combines accurate quantification of 2D limb bud morphologies and growth modeling to analyze mouse clonal data of early limb development. Firstly, we explore various tissue movements that match experimental limb bud shape changes. Secondly, by comparing computational clones with newly generated mouse clonal data we are able to choose and characterize the tissue movement map that better matches experimental data. Our computational analysis produces for the first time a two dimensional model of limb growth based on experimental data that can be used to better characterize limb tissue movement in space and time. The model shows that the distribution and shapes of clones can be described as a combination of anisotropic growth with isotropic cell mixing, without the need for lineage compartmentalization along the AP and PD axis. Lastly, we show that this comprehensive description can be used to reassess spatio-temporal gene regulations taking tissue movement into account and to investigate PD patterning hypothesis
Conditional Ablation of Ezh2 in Murine Hearts Reveals Its Essential Roles in Endocardial Cushion Formation, Cardiomyocyte Proliferation and Survival
Ezh2 is a histone trimethyltransferase that silences genes mainly via catalyzing trimethylation of histone 3 lysine 27 (H3K27Me3). The role of Ezh2 as a regulator of gene silencing and cell proliferation in cancer development has been extensively investigated; however, its function in heart development during embryonic cardiogenesis has not been well studied. In the present study, we used a genetically modified mouse system in which Ezh2 was specifically ablated in the mouse heart. We identified a wide spectrum of cardiovascular malformations in the Ezh2 mutant mice, which collectively led to perinatal death. In the Ezh2 mutant heart, the endocardial cushions (ECs) were hypoplastic and the endothelial-to-mesenchymal transition (EMT) process was impaired. The hearts of Ezh2 mutant mice also exhibited decreased cardiomyocyte proliferation and increased apoptosis. We further identified that the Hey2 gene, which is important for cardiomyocyte proliferation and cardiac morphogenesis, is a downstream target of Ezh2. The regulation of Hey2 expression by Ezh2 may be independent of Notch signaling activity. Our work defines an indispensible role of the chromatin remodeling factor Ezh2 in normal cardiovascular development
Characterization of inpaint residuals in interferometric measurements of the epoch of reionization
To mitigate the effects of Radio Frequency Interference (RFI) on the data analysis pipelines of 21 cm interferometric instruments, numerous inpaint techniques have been developed. In this paper, we examine the qualitative and quantitative errors introduced into the visibilities and power spectrum due to inpainting. We perform our analysis on simulated data as well as real data from the Hydrogen Epoch of Reionization Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural network that is capable of inpainting RFI corrupted data. We train our network on simulated data and show that our network is capable of inpainting real data without requiring to be retrained. We find that techniques that incorporate high wavenumbers in delay space in their modelling are best suited for inpainting over narrowband RFI. We show that with our fiducial parameters discrete prolate spheroidal sequences (DPSS) and CLEAN provide the best performance for intermittent RFI while Gaussian progress regression (GPR) and least squares spectral analysis (LSSA) provide the best performance for larger RFI gaps. However, we caution that these qualitative conclusions are sensitive to the chosen hyperparameters of each inpainting technique. We show that all inpainting techniques reliably reproduce foreground dominated modes in the power spectrum. Since the inpainting techniques should not be capable of reproducing noise realizations, we find that the largest errors occur in the noise dominated delay modes. We show that as the noise level of the data comes down, CLEAN and DPSS are most capable of reproducing the fine frequency structure in the visibilities
Impact of instrument and data characteristics in the interferometric reconstruction of the 21 cm power spectrum
Combining the visibilities measured by an interferometer to form a cosmological power spectrum is a complicated process. In a delay-based analysis, the mapping between instrumental 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 measured by an interferometer, we assess the impact of instrument characteristics and analysis choices on these window functions. Focusing on the Hydrogen Epoch of Reionization Array (HERA) as a case study, we find that long-baseline observations correspond to enhanced low-k tails of the window functions, which facilitate foreground leakage, whilst an informed choice of bandwidth and frequency taper can reduce said tails. With simple test cases and realistic simulations, we show that, apart from tracing mode mixing, the window functions help accurately reconstruct the power spectrum estimator of simulated visibilities. The window functions depend strongly on the beam chromaticity 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 here 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 will be used in future analyses to confront theoretical models and data directly in cylindrical space
Improved Constraints on the 21 cm EoR Power Spectrum and the X-Ray Heating of the IGM with HERA Phase I Observations
We report the most sensitive upper limits to date on the 21 cm epoch of reionization power spectrum using 94 nights of observing with Phase I of the Hydrogen Epoch of Reionization Array (HERA). Using similar analysis techniques as in previously reported limits, we find at 95% confidence that Δ2(k = 0.34 h Mpc−1) ≤ 457 mK2 at z = 7.9 and that Δ2(k = 0.36 h Mpc−1) ≤ 3496 mK2 at z = 10.4, an improvement by a factor of 2.1 and 2.6, respectively. These limits are mostly consistent with thermal noise over a wide range of k after our data quality cuts, despite performing a relatively conservative analysis designed to minimize signal loss. Our results are validated with both statistical tests on the data and end-to-end pipeline simulations. We also report updated constraints on the astrophysics of reionization and the cosmic dawn. Using multiple independent modeling and inference techniques previously employed by HERA Collaboration, we find that the intergalactic medium must have been heated above the adiabatic cooling limit at least as early as z = 10.4, ruling out a broad set of so-called “cold reionization” scenarios. If this heating is due to high-mass X-ray binaries during the cosmic dawn, as is generally believed, our result’s 99% credible interval excludes the local relationship between soft X-ray luminosity and star formation and thus requires heating driven by evolved low-metallicity stars
Direct Optimal Mapping for 21cm Cosmology: A Demonstration with the Hydrogen Epoch of Reionization Array
Motivated by the desire for wide-field images with well-defined statistical
properties for 21cm cosmology, we implement an optimal mapping pipeline that
computes a maximum likelihood estimator for the sky using the interferometric
measurement equation. We demonstrate this direct optimal mapping with data from
the Hydrogen Epoch of Reionization (HERA) Phase I observations. After
validating the pipeline with simulated data, we develop a maximum likelihood
figure-of-merit for comparing four sky models at 166MHz with a bandwidth of
100kHz. The HERA data agree with the GLEAM catalogs to <10%. After subtracting
the GLEAM point sources, the HERA data discriminate between the different
continuum sky models, providing most support for the model of Byrne et al.
2021. We report the computation cost for mapping the HERA Phase I data and
project the computation for the HERA 320-antenna data; both are feasible with a
modern server. The algorithm is broadly applicable to other interferometers and
is valid for wide-field and non-coplanar arrays.Comment: 16 pages, 10 figures, 2 tables, published on Ap
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
Characterization Of Inpaint Residuals In Interferometric Measurements of the Epoch Of Reionization
Radio Frequency Interference (RFI) is one of the systematic challenges
preventing 21cm interferometric instruments from detecting the Epoch of
Reionization. To mitigate the effects of RFI on data analysis pipelines,
numerous inpaint techniques have been developed to restore RFI corrupted data.
We examine the qualitative and quantitative errors introduced into the
visibilities and power spectrum due to inpainting. We perform our analysis on
simulated data as well as real data from the Hydrogen Epoch of Reionization
Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural
network that capable of inpainting RFI corrupted data in interferometric
instruments. We train our network on simulated data and show that our network
is capable at inpainting real data without requiring to be retrained. We find
that techniques that incorporate high wavenumbers in delay space in their
modeling are best suited for inpainting over narrowband RFI. We also show that
with our fiducial parameters Discrete Prolate Spheroidal Sequences (DPSS) and
CLEAN provide the best performance for intermittent ``narrowband'' RFI while
Gaussian Progress Regression (GPR) and Least Squares Spectral Analysis (LSSA)
provide the best performance for larger RFI gaps. However we caution that these
qualitative conclusions are sensitive to the chosen hyperparameters of each
inpainting technique. We find these results to be consistent in both simulated
and real visibilities. We show that all inpainting techniques reliably
reproduce foreground dominated modes in the power spectrum. Since the
inpainting techniques should not be capable of reproducing noise realizations,
we find that the largest errors occur in the noise dominated delay modes. We
show that in the future, as the noise level of the data comes down, CLEAN and
DPSS are most capable of reproducing the fine frequency structure in the
visibilities of HERA data.Comment: 26 pages, 18 figure
Direct Optimal Mapping Image Power Spectrum and its Window Functions
The key to detecting neutral hydrogen during the epoch of reionization (EoR)
is to separate the cosmological signal from the dominating foreground
radiation. We developed direct optimal mapping (Xu et al. 2022) to map
interferometric visibilities; it contains only linear operations, with full
knowledge of point spread functions from visibilities to images. Here we
present an FFT-based image power spectrum and its window functions based on
direct optimal mapping. We use noiseless simulation, based on the Hydrogen
Epoch of Reionization Array (HERA) Phase I configuration, to study the image
power spectrum properties. The window functions show power leakage
from the foreground-dominated region into the EoR window; the 2D and 1D power
spectra also verify the separation between the foregrounds and the EoR.
Furthermore, we simulated visibilities from a -complete array and
calculated its image power spectrum. The result shows that the foreground--EoR
leakage is further suppressed below , dominated by the tapering
function sidelobes; the 2D power spectrum does not show signs of the horizon
wedge. The -complete result provides a reference case for future 21cm
cosmology array designs.Comment: Submitted to Ap
Search for the Epoch of Reionisation with HERA: Upper Limits on the Closure Phase Delay Power Spectrum
Radio interferometers aiming to measure the power spectrum of the redshifted
21 cm line during the Epoch of Reionisation (EoR) need to achieve an
unprecedented dynamic range to separate the weak signal from overwhelming
foreground emissions. Calibration inaccuracies can compromise the sensitivity
of these measurements to the effect that a detection of the EoR is precluded.
An alternative to standard analysis techniques makes use of the closure phase,
which allows one to bypass antenna-based direction-independent calibration.
Similarly to standard approaches, we use a delay spectrum technique to search
for the EoR signal. Using 94 nights of data observed with Phase I of the
Hydrogen Epoch of Reionization Array (HERA), we place approximate constraints
on the 21 cm power spectrum at . We find at 95% confidence that the 21
cm EoR brightness temperature is (372) "pseudo" mK at 1.14
"pseudo" Mpc, where the "pseudo" emphasises that these limits are to
be interpreted as approximations to the actual distance scales and brightness
temperatures. Using a fiducial EoR model, we demonstrate the feasibility of
detecting the EoR with the full array. Compared to standard methods, the
closure phase processing is relatively simple, thereby providing an important
independent check on results derived using visibility intensities, or related.Comment: 16 pages, 14 figures, accepted for publication by MNRA
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