159 research outputs found
Differential strengths of selection on S-RNases from Physalis and Solanum (Solanaceae)
<p>Abstract</p> <p>Background</p> <p>The S-RNases of the Solanaceae are highly polymorphic self-incompatibility (S-) alleles subject to strong balancing selection. Relatively recent diversification of S-alleles has occurred in the genus <it>Physalis </it>following a historical restriction of S-allele diversity. In contrast, the genus <it>Solanum </it>did not undergo a restriction of S-locus diversity and its S-alleles are generally much older. Because recovery from reduced S-locus diversity should involve increased selection, we employ a statistical framework to ask whether S-locus selection intensities are higher in <it>Physalis </it>than <it>Solanum</it>. Because different S-RNase lineages diversify in <it>Physalis </it>and <it>Solanum</it>, we also ask whether different sites are under selection in different lineages.</p> <p>Results</p> <p>Maximum-likelihood and Bayesian coalescent methods found higher intensities of selection and more sites under significant positive selection in the 48 <it>Physalis </it>S-RNase alleles than the 49 from <it>Solanum</it>. Highest posterior densities of dN/dS (ω) estimates show that the strength of selection is greater for <it>Physalis </it>at 36 codons. A nested maximum likelihood method was more conservative, but still found 16 sites with greater selection in <it>Physalis</it>. Neither method found any codons under significantly greater selection in <it>Solanum</it>. A random effects likelihood method that examines data from both taxa jointly confirmed higher selection intensities in <it>Physalis</it>, but did not find different proportions of sites under selection in the two datasets. The greatest differences in strengths of selection were found in the most variable regions of the S-RNases, as expected if these regions encode self-recognition specificities. Clade-specific likelihood models indicated some codons were under greater selection in background <it>Solanum </it>lineages than in specific lineages of <it>Physalis </it>implying that selection on sites may differ among lineages.</p> <p>Conclusions</p> <p>Likelihood and Bayesian methods provide a statistical approach to testing differential selection across populations or species. These tests appear robust to the levels of polymorphism found in diverse S-allele collections subject to strong balancing selection. As predicted, the intensity of selection at the S-locus was higher in the taxon with more recent S-locus diversification. This is the first confirmation by statistical test of differing selection intensities among self-incompatibility alleles from different populations or species.</p
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
Characterizing Signal Loss in the 21 cm Reionization Power Spectrum: A Revised Study of PAPER-64
The Epoch of Reionization (EoR) is an uncharted era in our Universe's history
during which the birth of the first stars and galaxies led to the ionization of
neutral hydrogen in the intergalactic medium. There are many experiments
investigating the EoR by tracing the 21cm line of neutral hydrogen. Because
this signal is very faint and difficult to isolate, it is crucial to develop
analysis techniques that maximize sensitivity and suppress contaminants in
data. It is also imperative to understand the trade-offs between different
analysis methods and their effects on power spectrum estimates. Specifically,
with a statistical power spectrum detection in HERA's foreseeable future, it
has become increasingly important to understand how certain analysis choices
can lead to the loss of the EoR signal. In this paper, we focus on signal loss
associated with power spectrum estimation. We describe the origin of this loss
using both toy models and data taken by the 64-element configuration of the
Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER).
In particular, we highlight how detailed investigations of signal loss have led
to a revised, higher 21cm power spectrum upper limit from PAPER-64.
Additionally, we summarize errors associated with power spectrum error
estimation that were previously unaccounted for. We focus on a subset of
PAPER-64 data in this paper; revised power spectrum limits from the PAPER
experiment are presented in a forthcoming paper by Kolopanis et al. (in prep.)
and supersede results from previously published PAPER analyses.Comment: 25 pages, 18 figures, Accepted by Ap
The Hydrogen Epoch of Reionization Array Dish I: Beam Pattern Measurements and Science Implications
The Hydrogen Epoch of Reionization Array (HERA) is a radio interferometer
aiming to detect the power spectrum of 21 cm fluctuations from neutral hydrogen
from the Epoch of Reionization (EOR). Drawing on lessons from the Murchison
Widefield Array (MWA) and the Precision Array for Probing the Epoch of
Reionization (PAPER), HERA is a hexagonal array of large (14 m diameter) dishes
with suspended dipole feeds. Not only does the dish determine overall
sensitivity, it affects the observed frequency structure of foregrounds in the
interferometer. This is the first of a series of four papers characterizing the
frequency and angular response of the dish with simulations and measurements.
We focus in this paper on the angular response (i.e., power pattern), which
sets the relative weighting between sky regions of high and low delay, and
thus, apparent source frequency structure. We measure the angular response at
137 MHz using the ORBCOMM beam mapping system of Neben et al. We measure a
collecting area of 93 m^2 in the optimal dish/feed configuration, implying
HERA-320 should detect the EOR power spectrum at z~9 with a signal-to-noise
ratio of 12.7 using a foreground avoidance approach with a single season of
observations, and 74.3 using a foreground subtraction approach. Lastly we study
the impact of these beam measurements on the distribution of foregrounds in
Fourier space.Comment: 13 pages, 9 figures. Replaced to match accepted ApJ versio
The Hydrogen Epoch of Reionization Array Dish II: Characterization of Spectral Structure with Electromagnetic Simulations and its science Implications
We use time-domain electromagnetic simulations to determine the spectral
characteristics of the Hydrogen Epoch of Reionization Arrays (HERA) antenna.
These simulations are part of a multi-faceted campaign to determine the
effectiveness of the dish's design for obtaining a detection of redshifted 21
cm emission from the epoch of reionization. Our simulations show the existence
of reflections between HERA's suspended feed and its parabolic dish reflector
that fall below -40 dB at 150 ns and, for reasonable impedance matches, have a
negligible impact on HERA's ability to constrain EoR parameters. It follows
that despite the reflections they introduce, dishes are effective for
increasing the sensitivity of EoR experiments at relatively low cost. We find
that electromagnetic resonances in the HERA feed's cylindrical skirt, which is
intended to reduce cross coupling and beam ellipticity, introduces significant
power at large delays ( dB at 200 ns) which can lead to some loss of
measurable Fourier modes and a modest reduction in sensitivity. Even in the
presence of this structure, we find that the spectral response of the antenna
is sufficiently smooth for delay filtering to contain foreground emission at
line-of-sight wave numbers below Mpc, in
the region where the current PAPER experiment operates. Incorporating these
results into a Fisher Matrix analysis, we find that the spectral structure
observed in our simulations has only a small effect on the tight constraints
HERA can achieve on parameters associated with the astrophysics of
reionization.Comment: Accepted to ApJ, 18 pages, 17 Figures. Replacement matches accepted
manuscrip
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
Challenges and opportunities for implementing integrated mental health care: a district level situation analysis from five low- and middle-income countries.
BACKGROUND: Little is known about how to tailor implementation of mental health services in low- and middle-income countries (LMICs) to the diverse settings encountered within and between countries. In this paper we compare the baseline context, challenges and opportunities in districts in five LMICs (Ethiopia, India, Nepal, South Africa and Uganda) participating in the PRogramme for Improving Mental health carE (PRIME). The purpose was to inform development and implementation of a comprehensive district plan to integrate mental health into primary care. METHODS: A situation analysis tool was developed for the study, drawing on existing tools and expert consensus. Cross-sectional information obtained was largely in the public domain in all five districts. RESULTS: The PRIME study districts face substantial contextual and health system challenges many of which are common across sites. Reliable information on existing treatment coverage for mental disorders was unavailable. Particularly in the low-income countries, many health service organisational requirements for mental health care were absent, including specialist mental health professionals to support the service and reliable supplies of medication. Across all sites, community mental health literacy was low and there were no models of multi-sectoral working or collaborations with traditional or religious healers. Nonetheless health system opportunities were apparent. In each district there was potential to apply existing models of care for tuberculosis and HIV or non-communicable disorders, which have established mechanisms for detection of drop-out from care, outreach and adherence support. The extensive networks of community-based health workers and volunteers in most districts provide further opportunities to expand mental health care. CONCLUSIONS: The low level of baseline health system preparedness across sites underlines that interventions at the levels of health care organisation, health facility and community will all be essential for sustainable delivery of quality mental health care integrated into primary care
Improved 21 cm Epoch of Reionization Power Spectrum Measurements with a Hybrid Foreground Subtraction and Avoidance Technique
Observations of the 21 cm Epoch of Reionization signal are dominated by Galactic and extragalactic foregrounds. The need for foreground removal has led to the development of two main techniques, often referred to as “foreground avoidance” and “foreground subtraction.” Avoidance is associated with filtering foregrounds in Fourier space, while subtraction uses an explicit foreground model that is removed. Using 1088 hr of data from the 64-element PAPER array, we demonstrate that subtraction of a foreground model prior to delay-space foreground filtering results in a modest but measurable improvement of the performance of the filter. This proof-of-concept result shows that improvement stems from the reduced dynamic range requirements needed for the foreground filter: subtraction of a foreground model reduces the total foreground power, so for a fixed dynamic range, the filter can push toward fainter limits. We also find that the choice of window function used in the foreground filter can have an appreciable affect on the performance near the edges of the observing band. We demonstrate these effects using a smaller 3 hr sampling of data from the MWA, and find that the hybrid filtering and subtraction removal approach provides similar improvements across the band as seen in the case with PAPER-64
Sublithospheric diamond ages and the supercontinent cycle.
Subduction related to the ancient supercontinent cycle is poorly constrained by mantle samples. Sublithospheric diamond crystallization records the release of melts from subducting oceanic lithosphere at 300-700 km depths1,2 and is especially suited to tracking the timing and effects of deep mantle processes on supercontinents. Here we show that four isotope systems (Rb-Sr, Sm-Nd, U-Pb and Re-Os) applied to Fe-sulfide and CaSiO3 inclusions within 13 sublithospheric diamonds from Juína (Brazil) and Kankan (Guinea) give broadly overlapping crystallization ages from around 450 to 650 million years ago. The intracratonic location of the diamond deposits on Gondwana and the ages, initial isotopic ratios, and trace element content of the inclusions indicate formation from a peri-Gondwanan subduction system. Preservation of these Neoproterozoic-Palaeozoic sublithospheric diamonds beneath Gondwana until its Cretaceous breakup, coupled with majorite geobarometry3,4, suggests that they accreted to and were retained in the lithospheric keel for more than 300 Myr during supercontinent migration. We propose that this process of lithosphere growth-with diamonds attached to the supercontinent keel by the diapiric uprise of depleted buoyant material and pieces of slab crust-could have enhanced supercontinent stability
- …