Genomic analysis of macro- and micro-evolution in the reptilia

Recent advances in high-throughput, genomic sequencing allow unprecedented insight into the evolution of biodiversity. Chapter 1 of this thesis is a phylogenetic study of 1,145 sequenced loci, isolated using a novel high-throughput sequence capture methodology to address the phylogenetic position of turtles within tetrapods. The results reported here unambiguously place turtles as sister to archosaurs and resolve this long-standing question. Chapter 2 investigates the genetic basis of colorful pigmentation in the Green anole (Anolis carolinensis) by sequencing complete transcriptomes from the green dorsal, white ventral and pink dewlap skin. Anoles comprise an adaptive radiation of more than 400 species and color plays a central role in their ecology and evolution, but little is known about the genetic basis of colorful pigmentation in any vertebrate. This study identified 1,719 differentially expressed genes among the three differently colored tissues. Twenty-three of these genes are involved in melanin, pteridine, and carotenoid pigmentation pathways that contribute to the coloration of anole skin. Identifying candidate genes for colorful pigmentation is a significant advance that opens the field for comparative analysis in other taxa. To determine if the genes identified in Chapter 2 are involved in population divergence and speciation, Chapter 3 investigates the complete genomes of twenty individuals from two closely related subspecies of Anolis marmoratus. While the two subspecies differ markedly in pigmentation, this study found few genetic differences between populations except in five regions of the genome, which together contained 447 genes. Of these genes, only two, melanophilin (mlph) and 'cluster of differentiation 36' (cd36), are associated with pigmentation. The intersection of the genes identified in Chapter 2 and Chapter 3 includes both cd36 and mlph, suggesting that both are involved in divergence of coloration. Cd36 is of particular interest because it regulates the uptake of carotenoid pigments and is an important candidate gene contributing to carotenoid pigmentation. Together, this research demonstrates the power of genomic approaches to address fundamental questions in systematics, micro-evolution, and speciation. The findings bolster the emerging field of phylogenomics and broadly impact future research into the genetic basis of coloration in vertebrates

Optimization of the Ballistic Guide Design for the SNS FNPB 8.9 A Neutron Line

The optimization of the ballistic guide design for the SNS Fundamental Neutron Physics Beamline 8.9 A line is described. With a careful tuning of the shape of the curve for the tapered section and the width of the straight section, this optimization resulted in more than 75% increase in the neutron flux exiting the 33 m long guide over a straight m=3.5 guide with the same length.Comment: 21 pages, 13 figures; added a paragraph on existing ballistic guides to respond to referee comments; accepted for publication in Nuclear Inst. and Methods in Physics Research,

Developing an Inflatable Solar Array

L\u27Garde is developing a light weight deployable solar array wing in the 200-1000 watt range, on the Inflatable Torus Solar Array Technology Demonstration (ITSAT Demo) Project. The power density goal is 90-100 W/Kg for a 200 W wing, including structure and deployment mechanisms. In Phase 1, a proof of concept torus and array was constructed and deployed in the laboratory. A revised Phase 2 Torus and Array are now being fabricated. Phase 3 will be a space flight test. The current design uses crystalline Si cells on an A0 protected flexible Kapton film substrate folded accordion style for stowage. The support structure is a rectangular frame comprised of two inflated cylinders, the array stowage box and its cover. The cylinders, flattened, folded and stored for launch, are deployed by inflating with N2 and rigidized by straining the cylinder laminate material controllably beyond the elastic limit. This array is designed for optimum power density but, due to availability, some of the components come from excess production runs. Because of this, the actual power density of the engineering prototype will be about 15% less than the base line program array, which uses 2.2 mil crystalline silicon cells, 4 diameter inflatable tubes, and a 4:1 aspect ratio. This project is funded by ARPA with technical management oversight by the Phillips Laboratory

Peculiar Hydrogen-deficient Carbon Stars: Strontium-Rich Stars and the s-Process

Context: R Coronae Borealis (RCB) variables and their non-variable counterparts, the dustless Hydrogen-Deficient Carbon (dLHdC) stars have been known to exhibit enhanced s-processed material on their surfaces, especially Sr, Y, and Ba. No comprehensive work has been done to explore the s-process in these types of stars, however one particular RCB star, U Aqr, has been under scrutiny for its extraordinary Sr enhancement. Aims: We aim to identify RCB and dLHdC stars that have significantly enhanced Sr abundances, such as U Aqr, and use stellar evolution models to begin to estimate the type of neutron exposure that occurs in a typical HdC star. Methods: We compare the strength of the Sr II 4077 $\AA$ spectral line to Ca II H to identify the new subclass of Sr-rich HdCs. We additionally use the structural and abundance information from existing RCB MESA models to calculate the neutron exposure parameter, $\tau$ Results: We identify six stars in the Sr-rich class. Two are RCBs, and four are dLHdCs. We additionally find that the preferred RCB MESA model has a neutron exposure $\tau$ ~ 0.1 mb$^{-1}$, which is lower than the estimated $\tau$ between 0.15 and 0.6 mb$^{-1}$ for the Sr-rich star U Aqr found in the literature. We find trends in the neutron exposure corresponding to He-burning shell temperature, metallicity, and assumed s-processing site. Conclusions: We have found a sub-class of 6 HdCs known as the Sr-rich class, which tend to lie in the halo, outside the typical distribution of RCBs and dLHdCs. We find that dLHdC stars are more likely to be Sr-rich than RCBs, with an occurrence rate of ~13\% for dLHdCs and ~2\% for RCBs. This is one of the first potential spectroscopic differences between RCBs and dLHdCs, along with dLHdCs having stronger surface abundances of $^{18}$O.Comment: 8 pages, submitted to A&

Modeling R Coronae Borealis Stars: Effects of He-Burning Shell Temperature and Metallicity

The R Coronae Borealis (RCB) stars are extremely hydrogen-deficient carbon stars which produce large amounts of dust, causing sudden deep declines in brightness. They are believed to be formed primarily through white dwarf mergers. In this paper, we use MESA to investigate how post-merger objects with a range of initial He-burning shell temperatures from 2.1 - 5.4 *10^8 K with solar and subsolar metallicities evolve into RCB stars. The most successful model of these has subsolar metallicity and an initial temperature near 3 *10^8 K. We find a strong dependence on initial He-burning shell temperature for surface abundances of elements involved in the CNO cycle, as well as differences in effective temperature and radius of RCBs. Elements involved in nucleosynthesis present around 1 dex diminished surface abundances in the 10% solar metallicity models, with the exception of carbon and lithium which are discussed in detail. Models with subsolar metallicities also exhibit longer lifetimes than their solar counterparts. Additionally, we find that convective mixing of the burned material occurs only in the first few years of post-merger evolution, after which the surface abundances are constant during and after the RCB phase, providing evidence for why these stars show a strong enhancement of partial He-burning products.Comment: 13 pages, 12 figures, accepted to MNRAS on August 15, 202

R Coronae Borealis Star Evolution: Simulating 3D Merger Events to 1D Stellar Evolution Including Large Scale Nucleosynthesis

R Coronae Borealis (RCB) stars are rare hydrogen-deficient carbon-rich variable supergiants thought to be the result of dynamically unstable white dwarf mergers. We attempt to model RCBs through all the relevant timescales by simulating a merger event in Octo-tiger, a 3D adaptive mesh refinement (AMR) hydrodynamics code and mapping the post-merger object into MESA, a 1D stellar evolution code. We then post-process the nucleosynthesis on a much larger nuclear reaction network to study the enhancement of s-process elements. We present models that match observations or previous studies in most surface abundances, isotopic ratios, early evolution and lifetimes. We also observe similar mixing behavior as previous modeling attempts which result in the partial He-burning products visible on the surface in observations. However, we do note that our sub-solar models lack any enhancement in s-process elements, which we attribute to a lack of hydrogen in the envelope. We also find that the Oxygen-16/Oxygen-18 isotopic ratio is very sensitive to initial hydrogen abundance and increases outside of the acceptable range with a hydrogen mass fraction greater than $10^{-4}$.Comment: 18 pages, 17 figures, 1 table. To be published in The Astrophysical Journa

A Spectral Classification System for Hydrogen-deficient Carbon Stars

Stellar spectral classification, and especially the Yerkes system, has been highly useful in the study of stars. While there is a currently accepted classification system for carbon stars, the subset of Hydrogen-deficient Carbon (HdC) stars has not been well described by such a system, due in part to their rarity and their variability. Here we present a new system for the classification of HdCs based on their spectra, which is made wholly on their observable appearance. We use a combination of dimensionality reduction and clustering algorithms with human classification to create such a system. We classify over half of the known sample of HdC stars using this, and roughly calibrate the temperatures of each class using their colors. Additionally, we express trends in the occurrence of certain spectral peculiarities such as the presence of Hydrogen and Lithium lines. We also present three previously unpublished spectra, and report the discovery of three new Galactic dustless HdC (dLHdC) stars and additionally discuss one especially unique star that appears to border between the hottest HdCs and the coolest Extreme Helium (EHe) stars.Comment: 30 pages, 18 figures, submitted to MNRA

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

Efficacy of the Quickert procedure for involutional entropion : the first case series in Asia

Purpose : To report the efficacy of the Quickert procedure in the first case series of involutional entropion in an elderly Asian population, and to introduce the technique to Asian ophthalmologists including general ophthalmologisits and ophthalmic trainees. Methods : We conducted a retrospective review of 13 consecutive patients underwent the Quickert procedure for involutional entropion by occasional eyelid surgeons at Tokushima University Hospital or Mino Tanaka Hospital from September 2003 to April 2010. Demographic data, including gender, age, history of previous eyelid surgery, systemic disease, recurrence of entropion, postoperative complications, and symptoms were analyzed. Results : There were 5 male (38.5%) and 8 female (61.5%) subjects with a mean age of 77.8 years. Three patients underwent previous surgery for entropion were included. Entropion was rectified in all patients by a single Quickert procedure, and no recurrence was observed for a maximum of 89 months after the surgery. Although notching of the eyelid margin and mild symblepharon were observed in one patient, no symptoms associated with these complications were reported. Conclusion : The Quickert procedure can be one of the surgical procedures of choice for involutional entropion and should be common surgical approach for occasional eyelid surgeons in Asia as well as in western countries