Incorporating Uncertainties in Atomic Data Into the Analysis of Solar and Stellar Observations: A Case Study in Fe XIII

Information about the physical properties of astrophysical objects cannot be measured directly but is inferred by interpreting spectroscopic observations in the context of atomic physics calculations. Ratios of emission lines, for example, can be used to infer the electron density of the emitting plasma. Similarly, the relative intensities of emission lines formed over a wide range of temperatures yield information on the temperature structure. A critical component of this analysis is understanding how uncertainties in the underlying atomic physics propagates to the uncertainties in the inferred plasma parameters. At present, however, atomic physics databases do not include uncertainties on the atomic parameters and there is no established methodology for using them even if they did. In this paper we develop simple models for the uncertainties in the collision strengths and decay rates for Fe XIII and apply them to the interpretation of density sensitive lines observed with the EUV Imagining spectrometer (EIS) on Hinode. We incorporate these uncertainties in a Bayesian framework. We consider both a pragmatic Bayesian method where the atomic physics information is unaffected by the observed data, and a fully Bayesian method where the data can be used to probe the physics. The former generally increases the uncertainty in the inferred density by about a factor of 5 compared with models that incorporate only statistical uncertainties. The latter reduces the uncertainties on the inferred densities, but identifies areas of possible systematic problems with either the atomic physics or the observed intensities.Comment: in press at Ap

A revolute joint with linear load-displacement response for a deployable lidar telescope

NASA Langley Research Center is developing concepts for an advanced spacecraft, called LidarTechSat, to demonstrate key structures and mechanisms technologies necessary to deploy a segmented telescope reflector. Achieving micron-accuracy deployment requires significant advancements in deployment mechanism design, such as the revolute joint presented herein. The joint exhibits load-cycling response that is essentially linear with less than 2% hysteresis, and the joint rotates with less than 7 mN-m (1 in-oz) of resistance. A prototype reflector metering truss incorporating the joint exhibits only a few microns of kinematic error under repected deployment and impulse loading. No other mechanically deployment structure found in the literature has been demonstrated to be this kinematically accurate

Breeding Sustainable Beef Cows: Reducing Weight and Increasing Productivity

Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions. Cumulative weight weaned reflects reproductive performance and avoidance of premature culling for characteristics related to animal health, welfare, and worker safety. Both traits were evaluated with random regression models with records from a crossbred population representing 18 breeds that conduct US national cattle evaluations. The genomic REML analyses included additive and dominance components, with relationships among 22,776 animals constructed from genotypes of 181,286 potentially functional variants imputed from a low-pass sequence. Projected to 8 years of age, the additive heritability estimate for CW was 0.57 and 0.11 for WtW. Dominance heritability was 0.02 for CW and 0.19 for WtW. Many variants with significant associations with CW were within previously described quantitative trait loci (QTL) for growthrelated production, meat, and carcass traits. Significant additive WtW variants were covered by QTL for traits related to reproduction and structural soundness. All breeds contributed to groups of cows with high and low total genetic values (additive + dominance effects) for both traits. The high WtW cows and cows above the WtW mean but below the CW mean had larger heterosis values and fewer bases in runs of homozygosity. The high additive heritability of CW and dominance effects on WtW indicate that breeding to improve beef cow sustainability should involve selection to reduce CW and mate selection to maintain heterosis and reduce runs of homozygosity. Simple Summary: Improving the sustainability of beef cows involves reducing feed costs and enteric methane emissions and increasing calf production while addressing concerns including animal health and welfare and worker safety. Reducing cow weight can favorably impact feed costs and methane emissions. Cumulative weight weaned observed throughout a cow’s productive life directly addresses calf production and indirectly addresses other concerns—cumulative production is higher for cows who wean healthy calves and avoid culling because of reproductive failure, unsoundness, and dangerous behavior. Using functional variant genotypes imputed from the low-coverage whole genome sequence, this examination of cow weight and cumulative weight weaned in a herd of crossbred cattle resulted in additive heritability estimates of 0.57 for cow weight and 0.11 for weight weaned by 8-year-old cows. Corresponding dominance heritability estimates were 0.02 for cow weight and 0.19 for weight weaned. All breeds were represented by cows projected to have high and low cow weights and weight weaned. Heterosis was higher and genomic inbreeding, measured by runs of homozygosity, was lower among high-weight weaned cows. These results suggest selection should be effective in reducing cow weight. Selection to increase weight weaned will be slow but can be hastened with crossbreeding. Especially when pedigree is not available to estimate heterosis, runs of homozygosity may be a useful indicator of heterosis and a predictor of cumulative productivity. Beef cow sustainability can be improved with appropriate crossbreeding and selection, and may be accelerated by incorporating functional variants associated with sustainability-related traits

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease

Copyright: © 2013 Eyre et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedClostridium difficile whole genome sequencing has the potential to identify related isolates, even among otherwise indistinguishable strains, but interpretation depends on understanding genomic variation within isolates and individuals.Serial isolates from two scenarios were whole genome sequenced. Firstly, 62 isolates from 29 timepoints from three in vitro gut models, inoculated with a NAP1/027 strain. Secondly, 122 isolates from 44 patients (2–8 samples/patient) with mostly recurrent/on-going symptomatic NAP-1/027 C. difficile infection. Reference-based mapping was used to identify single nucleotide variants (SNVs).Across three gut model inductions, two with antibiotic treatment, total 137 days, only two new SNVs became established. Pre-existing minority SNVs became dominant in two models. Several SNVs were detected, only present in the minority of colonies at one/two timepoints. The median (inter-quartile range) [range] time between patients’ first and last samples was 60 (29.5–118.5) [0–561] days. Within-patient C. difficile evolution was 0.45 SNVs/called genome/year (95%CI 0.00–1.28) and within-host diversity was 0.28 SNVs/called genome (0.05–0.53). 26/28 gut model and patient SNVs were non-synonymous, affecting a range of gene targets.The consistency of whole genome sequencing data from gut model C. difficile isolates, and the high stability of genomic sequences in isolates from patients, supports the use of whole genome sequencing in detailed transmission investigations.Peer reviewe

Coyote Diets on the Rolling Plains Quail Research Ranch, Texas

Predation is a major cause of mortality and nest failure for the northern bobwhite (Colinus virginianus) across its range. Coyotes (Canis latrans) are a potential predator of bobwhites and typically the most common mesocarnivore on bobwhite range in Texas. Few data exist regarding the importance of bobwhites in the coyote’s diet in the Rolling Plains of Texas. We describe the seasonal and annual diets of coyotes on the Rolling Plains Quail Research Ranch (RPQRR), Fisher County, Texas. The RPQRR encompasses 1,902 ha of rolling terrain consisting of ridges and mesquite (Prosopis glandulosa) dominated rangeland; other common shrubs include netleaf hackberry (Celtis laevigata), littleleaf sumac (Rhus microphylla), lotebush (Ziziphus obtusifolia), wolfberry (Lycium berlandieri), chittam (Bumrlia lanuginosa), catclaws (Acacia spp., Mimosa spp.), and agarito (Mahonia trifoliolata). Prickly pear (Opuntia spp.) is abundant on most sites. The study area received 58 and 64 cm of rainfall, respectively during 2009 and 2010, below the 30-year average of 76 cm for Fisher County, Texas. We collected, and examined 720 coyote scats from December 2008 to December 2010. Each scat was prepared for analysis by placing it inside a nylon mesh bag and washing it for 2 cycles in an automatic washing machine. We analyzed scat contents macroscopically and any guard hairs were analyzed microscopically to identify prey to genus. We also collected estimates of abundance for a range of potential food sources including bobwhites, small mammals, and insects. Preliminary analyses suggest coyotes were minor predators of quail and their diets mainly consisted of seasonally-available mast (e.g., tunas of prickly pear) and rodents. Variation in timing and amount of rainfall during our study allowed us to document how coyotes adjusted their diets to the resulting fluctuations in food availability (especially mast)

Natural fracture patterns at Swift Reservoir anticline, NW Montana : the influence of structural position and lithology from multiple observation scales

Acknowledgements We gratefully acknowledge constructive reviews by Amerigo Corradetti and an anonymous reviewer and thank Stefano Tavani for editorial handling. Adam J. Cawood is grateful to David Ferrill, Kevin Smart, and Paul Gillespie for helpful conversations about fracture patterns, although the data and interpretations shown here are of course the sole responsibility of the authors. This study was carried out as part of a University of Aberdeen doctoral programme supported by the Natural Environment Research Council (NERC) Centre for Doctoral Training in Oil and Gas. Additional funding for fieldwork was provided by the University of Aberdeen Fold–Thrust Research Group. Petroleum Experts (formerly Midland Valley Exploration) is acknowledged for allowing the academic use of Move 2016.1 software. Financial support This research has been supported by the Natural Environment Research Council (grant no. NE/M00578X/1).Peer reviewedPublisher PD