Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate ncRNAs

Eukaryotes contain short (∼80–200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. Here, we report the discovery and characterization of UCEs from 12 sequenced Drosophilaspecies. We identified 98 elements ≥80 bp long with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead we infer that they experience a level of selective constraint almost 10-fold higher compared with missense mutations in protein-coding sequences, which is substantially higher than that observed previously for human UCEs. About one-half of these Drosophila UCEs overlap the transcribed portion of genes, with many of those that are within coding sequences likely to correspond to sites of ADAR-dependent RNA editing. For the remaining UCEs that are in nongenic regions, we find that many are potentially capable of forming RNA secondary structures. Among ten chosen for further analysis, we discovered that the majority are transcribed in multiple tissues of Drosophila melanogaster. We conclude that Drosophilaspecies are rich with UCEs and that many of them may correspond to novel noncoding RNAs

Polarized Redundant-Baseline Calibration for 21 cm Cosmology Without Adding Spectral Structure

21 cm cosmology is a promising new probe of the evolution of visible matter in our universe, especially during the poorly-constrained Cosmic Dawn and Epoch of Reionization. However, in order to separate the 21 cm signal from bright astrophysical foregrounds, we need an exquisite understanding of our telescopes so as to avoid adding spectral structure to spectrally-smooth foregrounds. One powerful calibration method relies on repeated simultaneous measurements of the same interferometric baseline to solve for the sky signal and for instrumental parameters simultaneously. However, certain degrees of freedom are not constrained by asserting internal consistency between redundant measurements. In this paper, we review the origin of these "degeneracies" of redundant-baseline calibration and demonstrate how they can source unwanted spectral structure in our measurement and show how to eliminate that additional, artificial structure. We also generalize redundant calibration to dual-polarization instruments, derive the degeneracy structure, and explore the unique challenges to calibration and preserving spectral smoothness presented by a polarized measurement.Comment: 12 pages, 3 figures, updated to match the published MNRAS versio

A review of seismic observations of Kepler and K2-Observed sdBV stars

This paper reviews recent seismic findings from Kepler and K2 data. Using three years of short cadence Kepler (K1) data, it is possible to examine time evolution of pulsations in an unprecedented way. While K2 observations are shorter, only three months, they are important as they are finding more sdBV stars than K1 did. Most importantly, K2 is discovering more p-mode pulsators with coverage not possible to get from the ground

Improved remote sensing methods to detect northern wild rice (Zizania palustris L.)

Declining populations of Zizania palustris L. (northern wildrice, or wildrice) during the last century drives the demand for new and innovative techniques to support monitoring of this culturally and ecologically significant crop wild relative. We trained three wildrice detection models in R and Google Earth Engine using data from annual aquatic vegetation surveys in northern Minnesota. Three di erent training datasets, varying in the definition of wildrice presence, were combined with Landsat 8 Operational Land Imager (OLI) and Sentinel-1 C-band synthetic aperture radar (SAR) imagery to map wildrice in 2015 using random forests. Spectral predictors were derived from phenologically important time periods of emergence (June–July) and peak harvest (August–September). The range of the Vertical Vertical (VV) polarization between the two time periods was consistently the top predictor. Model outputs were evaluated using both point and area-based validation (polygon). While all models performed well in the point validation with percent correctly classified ranging from 83.8% to 91.1%, we found polygon validation necessary to comprehensively assess wildrice detection accuracy. Our practical approach highlights a variety of applications that can be applied to guide field excursions and estimate the extent of occurrence at landscape scales. Further testing and validation of the methods we present may support multiyear monitoring which is foundational for the preservation of wildrice for future generations

The Impact of Beam Variations on Power Spectrum Estimation for 21 cm Cosmology II: Mitigation of Foreground Systematics for HERA

One key challenge in detecting 21 cm cosmological signal at z > 6 is to separate the cosmological signal from foreground emission. This can be studied in a power spectrum space where the foreground is confined to low delay modes whereas the cosmological signal can spread out to high delay modes. When there is a calibration error, however, chromaticity of gain errors propagates to the power spectrum estimate and contaminates the modes for cosmological detection. The Hydrogen Epoch of Reionization Array (HERA) employs a high-precision calibration scheme using redundancy in measurements. In this study, we focus on the gain errors induced by nonredundancies arising from feed offset relative to the HERA's 14 meter parabolic dish element, and investigate how to mitigate the chromatic gain errors using three different methods: restricting baseline lengths for calibration, smoothing the antenna gains, and applying a temporal filter prior to calibration. With 2 cm/2 degree perturbations for translation/tilting motions, a level achievable under normal HERA operating conditions, the combination of the baseline cut and temporal filtering indicates that the spurious gain feature due to nonredundancies is significantly reduced, and the power spectrum recovers the clean foreground-free region. We found that the mitigation technique works even for large feed motions but in order to keep a stable calibration process, the feed positions need to be constrained to 2 cm for translation motions and 2 degree for tilting offset relative to the dish's vertex.Comment: Accepted for publication in Ap

Photoreversible interconversion of a phytochrome photosensory module in the crystalline state.

A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion

Scanning disk rings and winds in CO at 0.01-10 au: a high-resolution MM-band spectroscopy survey with IRTF-iSHELL

We present an overview and first results from a $M$-band spectroscopic survey of planet-forming disks performed with iSHELL on IRTF, using two slits that provide resolving power R $\approx$ 60,000-92,000 (5-3.3 km/s). iSHELL provides a nearly complete coverage at 4.52-5.24 $\mu$m in one shot, covering $>50$ lines from the R and P branches of $^{12}$CO and $^{13}$CO for each of multiple vibrational levels, and providing unprecedented information on the excitation of multiple emission and absorption components. Some of the most notable new findings of this survey are: 1) the detection of two CO Keplerian rings at $<2$ au (in HD 259431), 2) the detection of H${_2}$O ro-vibrational lines at 5 $\mu$m (in AS 205 N), and 3) the common kinematic variability of CO lines over timescales of 1-14 years. By homogeneously analyzing this survey together with a previous VLT-CRIRES survey of cooler stars, we discuss a unified view of CO spectra where emission and absorption components scan the disk surface across radii from a dust-free region within dust sublimation out to $\approx10$ au. We classify two fundamental types of CO line shapes interpreted as emission from Keplerian rings (double-peak lines) and a disk surface plus a low-velocity part of a wind (triangular lines), where CO excitation reflects different emitting regions (and their gas-to-dust ratio) rather than just the irradiation spectrum. A disk+wind interpretation for the triangular lines naturally explains several properties observed in CO spectra, including the line blue-shifts, line shapes that turn into narrow absorption at high inclinations, and the frequency of disk winds as a function of stellar type.Comment: Accepted for publication on The Astronomical Journa

Exploiting the ANN Potential in Estimating Snow Depth and Snow Water Equivalent From the Airborne SnowSAR Data at X- and Ku-Bands

Within the framework of European Space Agency (ESA) activities, several campaigns were carried out in the last decade with the purpose of exploiting the capabilities of multifrequency synthetic aperture radar (SAR) data to retrieve snow information. This article presents the results obtained from the ESA SnowSAR airborne campaigns, carried out between 2011 and 2013 on boreal forest, tundra and alpine environments, selected as representative of different snow regimes. The aim of this study was to assess the capability of X- and Ku-bands SAR in retrieving the snow parameters, namely snow depth (SD) and snow water equivalent (SWE). The retrieval was based on machine learning (ML) techniques and, in particular, of artificial neural networks (ANNs). ANNs have been selected among other ML approaches since they are capable to offer a good compromise between retrieval accuracy and computational cost. Two approaches were evaluated, the first based on the experimental data (data driven) and the second based on data simulated by the dense medium radiative transfer (DMRT). The data driven algorithm was trained on half of the SnowSAR dataset and validated on the remaining half. The validation resulted in a correlation coefficient R ≃ 0.77 between estimated and target SD, a root-mean-square error (RMSE) ≃ 13 cm, and bias = 0.03 cm. ANN algorithms specific for each test site were also implemented, obtaining more accurate results, and the robustness of the data driven approach was evaluated over time and space. The algorithm trained with DMRT simulations and tested on the experimental dataset was able to estimate the target parameter (SWE in this case) with R = 0.74, RMSE = 34.8 mm, and bias = 1.8 mm. The model driven approach had the twofold advantage of reducing the amount of in situ data required for training the algorithm and of extending the algorithm exportability to other test sites