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Open Access Publications from the University of California

Recent Works

A Broad Survey of Gene Body and Repeat Methylation in Cnidaria Reveals a Complex Evolutionary History.


DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.

A Machine Learning-based Direction-of-origin Filter for the Identification of Radio Frequency Interference in the Search for Technosignatures


Abstract Radio frequency interference (RFI) mitigation remains a major challenge in the search for radio technosignatures. Typical mitigation strategies include a direction-of-origin (DoO) filter, where a signal is classified as RFI if it is detected in multiple directions on the sky. These classifications generally rely on estimates of signal properties, such as frequency and frequency drift rate. Convolutional neural networks (CNNs) offer a promising complement to existing filters because they can be trained to analyze dynamic spectra directly, instead of relying on inferred signal properties. In this work, we compiled several data sets consisting of labeled pairs of images of dynamic spectra, and we designed and trained a CNN that can determine whether or not a signal detected in one scan is also present in another scan. This CNN-based DoO filter outperforms both a baseline 2D correlation model and existing DoO filters over a range of metrics, with precision and recall values of 99.15% and 97.81%, respectively. We found that the CNN reduces the number of signals requiring visual inspection after the application of traditional DoO filters by a factor of 6–16 in nominal situations.

Analysis of Four-band WISE Observations of Asteroids


Abstract We analyzed 82,548 carefully curated observations of 4420 asteroids with Wide-field Infrared Survey Explorer (WISE) four-band data to produce estimates of diameters and infrared emissivities. We also used these diameter values in conjunction with absolute visual magnitudes to infer estimates of visible-band geometric albedos. We provide solutions to 131 asteroids not analyzed by the NEOWISE team and to 1778 asteroids not analyzed with four-band data by the NEOWISE team. Our process differs from the NEOWISE analysis in that it uses an accurate solar flux, integrates the flux with actual bandpass responses, obeys Kirchhoff’s law, and does not force emissivity values in all four bands to an arbitrary value of 0.9. We used a regularized model-fitting algorithm that yields improved fits to the data. Our results more closely match stellar-occultation diameter estimates than the NEOWISE results by a factor of ∼2. Using 24 high-quality stellar-occultation results as a benchmark, we found that the median error of four-infrared-band diameter estimates in a carefully curated data set is 9.3%. Our results also suggest the presence of a size-dependent bias in the NEOWISE diameter estimates, which may pollute estimates of asteroid size distributions and slightly inflate impact-hazard risk calculations. For more than 90% of asteroids in this sample, the primary source of error on the albedo estimate is the error on absolute visual magnitude.

Spin state and moment of inertia of Venus


Fundamental properties of the planet Venus, such as its internal mass distribution and variations in length of day, have remained unknown. We used Earth-based observations of radar speckles tied to the rotation of Venus obtained in 2006-2020 to measure its spin axis orientation, spin precession rate, moment of inertia, and length-of-day variations. Venus is tilted by 2.6392 $\pm$ 0.0008 degrees ($1\sigma$) with respect to its orbital plane. The spin axis precesses at a rate of 44.58 $\pm$ 3.3 arcseconds per year ($1\sigma$), which gives a normalized moment of inertia of 0.337 $\pm$ 0.024 and yields a rough estimate of the size of the core. The average sidereal day on Venus in the 2006-2020 interval is 243.0226 $\pm$ 0.0013 Earth days ($1\sigma$). The spin period of the solid planet exhibits variations of 61 ppm ($\sim$20 minutes) with a possible diurnal or semidiurnal forcing. The length-of-day variations imply that changes in atmospheric angular momentum of at least $\sim$4% are transferred to the solid planet.

Cover page of InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards.

InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards.


Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth-system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ47) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ47 and Δ47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ47 (I-CDES) values for Intercarb-Carbon Dioxide Equilibrium Scale.

Cover page of Determining EMIC Wave Vector Properties Through Multi-Point Measurements: The Wave Curl Analysis.

Determining EMIC Wave Vector Properties Through Multi-Point Measurements: The Wave Curl Analysis.


Electromagnetic ion cyclotron (EMIC) waves play important roles in particle loss processes in the magnetosphere. Determining the evolution of EMIC waves as they propagate and how this evolution affects wave-particle interactions requires accurate knowledge of the wave vector, k. We present a technique using the curl of the wave magnetic field to determine k observationally, enabled by the unique configuration and instrumentation of the Magnetospheric MultiScale (MMS) spacecraft. The wave curl analysis is demonstrated for synthetic arbitrary electromagnetic waves with varying properties typical of observed EMIC waves. The method is also applied to an EMIC wave interval observed by MMS on October 28, 2015. The derived wave properties and k from the wave curl analysis for the observed EMIC wave are compared with the Waves in Homogenous, Anisotropic, Multi-component Plasma (WHAMP) wave dispersion solution and with results from other single- and multi-spacecraft techniques. We find good agreement between k from the wave curl analysis, k determined from other observational techniques, and k determined from WHAMP. Additionally, the variation of k due to the time and frequency intervals used in the wave curl analysis is explored. This exploration demonstrates that the method is robust when applied to a wave containing at least 3-4 wave periods and over a rather wide frequency range encompassing the peak wave emission. These results provide confidence that we are able to directly determine the wave vector properties using this multi-spacecraft method implementation, enabling systematic studies of EMIC wave k properties with MMS.

A Data-Taking System for Planetary Radar Applications


Most planetary radar applications require recording of complex voltages at sampling rates of up to 20[Formula: see text]MHz. I describe the design and implementation of a sampling system that has been installed at the Arecibo Observatory, Goldstone Solar System Radar, and Green Bank Telescope. After many years of operation, these data-taking systems have enabled the acquisition of hundreds of datasets, many of which still await publication.

Cover page of Gyroresonant wave-particle interactions with chorus waves during extreme depletions of plasma density in the Van Allen radiation belts.

Gyroresonant wave-particle interactions with chorus waves during extreme depletions of plasma density in the Van Allen radiation belts.


The Van Allen Probes mission provides unique measurements of the most energetic radiation belt electrons at ultrarelativistic energies. Simultaneous observations of plasma waves allow for the routine inference of total plasma number density, a parameter that is very difficult to measure directly. On the basis of long-term observations in 2015, we show that the underlying plasma density has a controlling effect over acceleration to ultrarelativistic energies, which occurs only when the plasma number density drops down to very low values (~10 cm-3). Such low density creates preferential conditions for local diffusive acceleration of electrons from hundreds of kilo-electron volts up to >7 MeV. While previous models could not reproduce the local acceleration of electrons to such high energies, here we complement the observations with a numerical model to show that the conditions of extreme cold plasma depletion result in acceleration up to >7 MeV.

Cover page of A search for technosignatures around 31 sun-like stars with the green bank telescope at 1.15-1.73 GHz

A search for technosignatures around 31 sun-like stars with the green bank telescope at 1.15-1.73 GHz


We conducted a search for technosignatures in 2018 and 2019 April with the L-band receiver (1.15-1.73 GHz) of the 100 m diameter Green Bank Telescope. These observations focused on regions surrounding 31 Sun-like stars near the plane of the Galaxy. We present the results of our search for narrowband signals in this data set, as well as improvements to our data processing pipeline. Specifically, we applied an improved candidate signal detection procedure that relies on the topographic prominence of the signal power, which nearly doubles the signal detection count of some previously analyzed data sets. We also improved the direction-of-origin filters that remove most radio frequency interference (RFI) to ensure that they uniquely link signals observed in separate scans. We performed a preliminary signal injection and recovery analysis to test the performance of our pipeline. We found that our pipeline recovers 93% of the injected signals over the usable frequency range of the receiver and 98% if we exclude regions with dense RFI. In this analysis, 99.73% of the recovered signals were correctly classified as technosignature candidates. Our improved data processing pipeline classified over 99.84% of the ∼26 million signals detected in our data as RFI. Of the remaining candidates, 4539 were detected outside of known RFI frequency regions. The remaining candidates were visually inspected and verified to be of anthropogenic nature. Our search compares favorably to other recent searches in terms of end-to-end sensitivity, frequency drift rate coverage, and signal detection count per unit bandwidth per unit integration time.

Cover page of Organic Material on Ceres: Insights from Visible and Infrared Space Observations.

Organic Material on Ceres: Insights from Visible and Infrared Space Observations.


The NASA/Dawn mission has acquired unprecedented measurements of the surface of the dwarf planet Ceres, the composition of which is a mixture of ultra-carbonaceous material, phyllosilicates, carbonates, organics, Fe-oxides, and volatiles as determined by remote sensing instruments including the VIR imaging spectrometer. We performed a refined analysis merging visible and infrared observations of Ceres' surface for the first time. The overall shape of the combined spectrum suggests another type of silicate not previously considered, and we confirmed a large abundance of carbon material. More importantly, by analyzing the local spectra of the organic-rich region of the Ernutet crater, we identified a reddening in the visible range, strongly correlated to the aliphatic signature at 3.4 µm. Similar reddening was found in the bright material making up Cerealia Facula in the Occator crater. This implies that organic material might be present in the source of the faculae, where brines and organics are mixed in an environment that may be favorable for prebiotic chemistry.