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Identifying the molecular underpinnings of the neural specializations that underlie human cognitive and behavioral traits has long been of considerable interest. Much research on human-specific changes in gene expression and epigenetic marks has focused on the prefrontal cortex, a brain structure distinguished by its role in executive functions. The cerebellum shows expansion in great apes and is gaining increasing attention for its role in motor skills and cognitive processing, including language. However, relatively few molecular studies of the cerebellum in a comparative evolutionary context have been conducted. Here, we identify human-specific methylation in the lateral cerebellum relative to the dorsolateral prefrontal cortex, in a comparative study with chimpanzees ( Pan troglodytes ) and rhesus macaques ( Macaca mulatta ). Specifically, we profiled genome-wide methylation levels in the three species for each of the two brain structures and identified human-specific differentially methylated genomic regions unique to each structure. We further identified which differentially methylated regions (DMRs) overlap likely regulatory elements and determined whether associated genes show corresponding species differences in gene expression. We found greater human-specific methylation in the cerebellum than the dorsolateral prefrontal cortex, with differentially methylated regions overlapping genes involved in several conditions or processes relevant to human neurobiology,more »including synaptic plasticity, lipid metabolism, neuroinflammation and neurodegeneration, and neurodevelopment, including developmental disorders. Moreover, our results show some overlap with those of previous studies focused on the neocortex, indicating that such results may be common to multiple brain structures. These findings further our understanding of the cerebellum in human brain evolution.« less

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 themore »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.

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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= 0.34hMpc⁻¹) ≤ 457 mK²atz= 7.9 and that Δ²(k= 0.36hMpc⁻¹) ≤ 3496 mK²atz= 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 ofkafter 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 asz= 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 relationshipmore »between soft X-ray luminosity and star formation and thus requires heating driven by evolved low-metallicity stars.

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We present a Bayesian jackknife test for assessing the probability that a data set contains biased subsets, and, if so, which of the subsets are likely to be biased. The test can be used to assess the presence and likely source of statistical tension between different measurements of the same quantities in an automated manner. Under certain broadly applicable assumptions, the test is analytically tractable. We also provide an open-source code, chiborg, that performs both analytic and numerical computations of the test on general Gaussian-distributed data. After exploring the information theoretical aspects of the test and its performance with an array of simulations, we apply it to data from the Hydrogen Epoch of Reionization Array (HERA) to assess whether different sub-seasons of observing can justifiably be combined to produce a deeper 21 cm power spectrum upper limit. We find that, with a handful of exceptions, the HERA data in question are statistically consistent and this decision is justified. We conclude by pointing out the wide applicability of this test, including to CMB experiments and the H0 tension.

Motivated by the desire for wide-field images with well-defined statistical properties for 21 cm 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 166 MHz with a bandwidth of 100 kHz. 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. 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 noncoplanar arrays.

Abstract We report upper limits on the Epoch of Reionization 21 cm power spectrum at redshifts 7.9 and 10.4 with 18 nights of data (∼36 hr of integration) from Phase I of the Hydrogen Epoch of Reionization Array (HERA). The Phase I data show evidence for systematics that can be largely suppressed with systematic models down to a dynamic range of ∼10 9 with respect to the peak foreground power. This yields a 95% confidence upper limit on the 21 cm power spectrum of Δ 21 2 ≤ ( 30.76 ) 2 mK 2 at k = 0.192 h Mpc −1 at z = 7.9, and also Δ 21 2 ≤ ( 95.74 ) 2 mK 2 at k = 0.256 h Mpc −1 at z = 10.4. At z = 7.9, these limits are the most sensitive to date by over an order of magnitude. While we find evidence for residual systematics at low line-of-sight Fourier k ∥ modes, at high k ∥ modes we find our data to be largely consistent with thermal noise, an indicator that the system could benefit from deeper integrations. The observed systematics could be due to radio frequency interference, cable subreflections, or residualmore »instrumental cross-coupling, and warrant further study. This analysis emphasizes algorithms that have minimal inherent signal loss, although we do perform a careful accounting in a companion paper of the small forms of loss or bias associated with the pipeline. Overall, these results are a promising first step in the development of a tuned, instrument-specific analysis pipeline for HERA, particularly as Phase II construction is completed en route to reaching the full sensitivity of the experiment.« less

Abstract We describe the validation of the HERA Phase I software pipeline by a series of modular tests, building up to an end-to-end simulation. The philosophy of this approach is to validate the software and algorithms used in the Phase I upper-limit analysis on wholly synthetic data satisfying the assumptions of that analysis, not addressing whether the actual data meet these assumptions. We discuss the organization of this validation approach, the specific modular tests performed, and the construction of the end-to-end simulations. We explicitly discuss the limitations in scope of the current simulation effort. With mock visibility data generated from a known analytic power spectrum and a wide range of realistic instrumental effects and foregrounds, we demonstrate that the current pipeline produces power spectrum estimates that are consistent with known analytic inputs to within thermal noise levels (at the 2 σ level) for k > 0.2 h Mpc −1 for both bands and fields considered. Our input spectrum is intentionally amplified to enable a strong “detection” at k ∼ 0.2 h Mpc −1 —at the level of ∼25 σ —with foregrounds dominating on larger scales and thermal noise dominating at smaller scales. Our pipeline is able to detect this amplifiedmore »input signal after suppressing foregrounds with a dynamic range (foreground to noise ratio) of ≳10 7 . Our validation test suite uncovered several sources of scale-independent signal loss throughout the pipeline, whose amplitude is well-characterized and accounted for in the final estimates. We conclude with a discussion of the steps required for the next round of data analysis.« less

ABSTRACT Precision calibration poses challenges to experiments probing the redshifted 21-cm signal of neutral hydrogen from the Cosmic Dawn and Epoch of Reionization (z ∼ 30–6). In both interferometric and global signal experiments, systematic calibration is the leading source of error. Though many aspects of calibration have been studied, the overlap between the two types of instruments has received less attention. We investigate the sky based calibration of total power measurements with a HERA dish and an EDGES-style antenna to understand the role of autocorrelations in the calibration of an interferometer and the role of sky in calibrating a total power instrument. Using simulations we study various scenarios such as time variable gain, incomplete sky calibration model, and primary beam model. We find that temporal gain drifts, sky model incompleteness, and beam inaccuracies cause biases in the receiver gain amplitude and the receiver temperature estimates. In some cases, these biases mix spectral structure between beam and sky resulting in spectrally variable gain errors. Applying the calibration method to the HERA and EDGES data, we find good agreement with calibration via the more standard methods. Although instrumental gains are consistent with beam and sky errors similar in scale to those simulated,more »the receiver temperatures show significant deviations from expected values. While we show that it is possible to partially mitigate biases due to model inaccuracies by incorporating a time-dependent gain model in calibration, the resulting errors on calibration products are larger and more correlated. Completely addressing these biases will require more accurate sky and primary beam models.« less