MS

thesisFive species of wild rodents native to the Great Salt Lake Basin have been found to produce a characteristic cutaneous response to intradermal injection of various Past. tularensis preparations, following challenge with viable Past. tularensis organisms. An area of in duration was produced which reached maximal size at 48 hours following intradermal injection of the Past. tularensis preparations. Histologically this reaction appeared to be a typical acute inflammatory process. Cutaneous sensitivity as a result of intradermal injection of heat killed Past. tularensis cells into challenged deer mice, Ord kangaroo rats, and desert wood rats persisted for up to 53, 40 and 25 weeks respectively. Deer mice challenged with Br. suis did not react to intradermal injection of heat killed Schu A strain cells whereas reactors were observed among deer mice challenged the Br. neotomae. White mice, guinea pigs and albino rabbits challenged with Past. tularensis were also observed to develop characteristic responses following intradermal injection of various Past. tularensis preparations. The cutaneous response of the challenged white mice was similar to that of the challenged wild rodents. In challenged guinea pigs the cutaneous response was one of edema and erythema which was maximal 24 hours after skin test. The response of rabbits to intradermal injection of Past. tularensis preparation was an erythematous area attaining a maximum size 48 hours after skin tests. The occurrence and development of cutaneous sensitivity in guinea pigs following challenge with Past. tularensis, strain Jap4, was studies. It was observed that cutaneous sensitivity may develop 4 to 5 days following challenge. Passive transfer studies with peritoneal exudate cells indicated a lack of detectable delayed hypersensitivity during the first week following challenge. However, delayed hypersensitivity was demonstrated in guinea pigs two, three and four weeks following challenge with the Jap4 strain Past. tularensis. A method of quantitative determination of Past. tularensis antibody precipitated by polysaccharide was established and used to determine the antibody nitrogen necessary to evoke local cutaneous sensitivity to Past. tularensis skin test antigens in normal rabbits and guinea pigs. Experimental evidence demonstrated that the cutaneous response of Past. tularensis challenged guinea pigs to intradermal injection of polysaccharide was similar to the Arthus type of reaction. It was also demonstrated that the cutaneous response of challenged guinea pigs to intradermal injections of heat killed Past. tularensis Schu A organisms was a combination of the Arthus type and the delayed type of hypersensitivity response. The persistence of Past. tularensis complement fixing and agglutinating antibodies in Past. tularensis Jap4 challenged deer mice, Ord kangaroo rats and wood rats was studied. The deer mice complement fixing antibody persisted for 31 weeks and agglutinating antibody for 25 weeks. Antibody detected by both tests persisted in Ord kangaroo rats for at least 40 weeks, although the agglutinin titers were much higher than the complement fixing titers. In challenged wood rats, both tests were positive in some animals 25 weeks following challenge. The relative values of the skin tests, agglutination test, and complement fixation test to detect Past. tularensis infection in rodents were discussed

Probing the Circumgalactic Medium at High-Redshift Using Composite BOSS Spectra of Strong Lyman-alpha Forest Absorbers

We present composite spectra constructed from a sample of 242,150 Lyman-alpha (Lya) forest absorbers at redshifts 2.4<z<3.1 identified in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) as part of Data Release 9 of the Sloan Digital Sky Survey III. We select forest absorbers by their flux in bins 138 km/s wide (approximately the size of the BOSS resolution element). We split these absorbers into five samples spanning the range of flux -0.05 < F<0.45. Tests on a smaller sample of high-resolution spectra show that our three strongest absorption bins would probe circumgalactic regions (projected separation < 300 proper kpc and |Delta v| < 300km/s) in about 60% of cases for very high signal-to-noise ratio. Within this subset, weakening Lya absorption is associated with decreasing purity of circumgalactic selection once BOSS noise is included. Our weaker two Lya absorption samples are dominated by the intergalactic medium. We present composite spectra of these samples and a catalogue of measured absorption features from HI and 13 metal ionization species, all of which we make available to the community. We compare measurements of seven Lyman series transitions in our composite spectra to single line models and obtain further constraints from their associated excess Lyman limit opacity. This analysis provides results consistent with column densities over the range 14.4 <~ Log (N_HI) <~ 16.45. We compare our measurements of metal absorption to a variety of simple single-line, single-phase models for a preliminary interpretation. Our results imply clumping on scales down to ~30 pc and near-solar metallicities in the circumgalactic samples, while high-ionization metal absorption consistent with typical IGM densities and metallicities is visible in all samples.Comment: 23 pages, 15 figures, 5 tables, link to downloadable data included. Accepted by MNRAS 2014 March 20. New sections 3.4 and 6.1 limiting the occurrence and impact of Lyman limit system

Galaxy clustering in the NEWFIRM Medium Band Survey: the relationship between stellar mass and dark matter halo mass at 1 < z < 2

We present an analysis of the clustering of galaxies as a function of their stellar mass at 1 < z < 2 using data from the NEWFIRM Medium Band Survey (NMBS). The precise photometric redshifts and stellar masses that the NMBS produces allows us to define a series of mass limited samples of galaxies more massive than 0.7, 1 and 3x10^10 Msun in redshift intervals centered on z = 1.1, 1.5 and 1.9 respectively. In each redshift interval we show that there exists a strong dependence of clustering strength on the stellar mass limit of the sample, with more massive galaxies showing a higher clustering amplitude on all scales. We further interpret our clustering measurements in the LCDM cosmological context using the halo model of galaxy clustering. We show that the typical halo mass of central and satellite galaxies increases with stellar mass, whereas the satellite fraction decreases with stellar mass, qualitatively the same as is seen at z < 1. We see little evidence of any redshift dependence in the stellar mass-to-halo mass relationship over our narrow redshift range. However, when we compare with similar measurements at z~0, we see clear evidence for a change in this relation. If we assume a universal baryon fraction, the ratio of stellar mass to halo mass reveals the fraction of baryons that have been converted to stars. We see that the peak in this star formation efficiency for central galaxies shifts to higher halo masses at higher redshift, moving from ~7x10^11 Msun at z~0 to ~3x10^12 Msun at z~1.5, revealing evidence of `halo downsizing'. Finally we show that for highly biased galaxy populations at z > 1 there may be a discrepancy between the measured space density and clustering and that predicted by the halo model. This could imply that there is a problem with one or more ingredients of the halo model at these redshifts, for instance the halo bias relation or the halo profile.Comment: Accepted for publication in ApJ. Correction made to typo in halo masses in conclusion

The SDSS-III Baryon Oscillation Spectroscopic Survey: Quasar Target Selection for Data Release Nine

The SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), a five-year spectroscopic survey of 10,000 deg^2, achieved first light in late 2009. One of the key goals of BOSS is to measure the signature of baryon acoustic oscillations in the distribution of Ly-alpha absorption from the spectra of a sample of ~150,000 z>2.2 quasars. Along with measuring the angular diameter distance at z\approx2.5, BOSS will provide the first direct measurement of the expansion rate of the Universe at z > 2. One of the biggest challenges in achieving this goal is an efficient target selection algorithm for quasars over 2.2 < z < 3.5, where their colors overlap those of stars. During the first year of the BOSS survey, quasar target selection methods were developed and tested to meet the requirement of delivering at least 15 quasars deg^-2 in this redshift range, out of 40 targets deg^-2. To achieve these surface densities, the magnitude limit of the quasar targets was set at g <= 22.0 or r<=21.85. While detection of the BAO signature in the Ly-alpha absorption in quasar spectra does not require a uniform target selection, many other astrophysical studies do. We therefore defined a uniformly-selected subsample of 20 targets deg^-2, for which the selection efficiency is just over 50%. This "CORE" subsample will be fixed for Years Two through Five of the survey. In this paper we describe the evolution and implementation of the BOSS quasar target selection algorithms during the first two years of BOSS operations. We analyze the spectra obtained during the first year. 11,263 new z>2.2 quasars were spectroscopically confirmed by BOSS. Our current algorithms select an average of 15 z > 2.2 quasars deg^-2 from 40 targets deg^-2 using single-epoch SDSS imaging. Multi-epoch optical data and data at other wavelengths can further improve the efficiency and completeness of BOSS quasar target selection. [Abridged]Comment: 33 pages, 26 figures, 12 tables and a whole bunch of quasars. Submitted to Ap

IGM constraints from the SDSS-III/BOSS DR9 Ly? forest transmission probability distribution function

© 2015. The American Astronomical Society. All rights reserved. The Lyα forest transmission probability distribution function (PDF) is an established probe of the intergalactic medium (IGM) astrophysics, especially the temperature-density relationship of the IGM. We measure the transmission PDF from 3393 Baryon Oscillations Spectroscopic Survey (BOSS) quasars from Sloan Digital Sky Survey Data Release 9, and compare with mock spectra that include careful modeling of the noise, continuum, and astrophysical uncertainties. The BOSS transmission PDFs, measured at 〈z〉 = [2.3, 2.6, 3.0], are compared with PDFs created from mock spectra drawn from a suite of hydrodynamical simulations that sample the IGM temperature-density relationship, γ, and temperature at mean density, T0, where T (Δ) = T0Δγ-1. We find that a significant population of partial Lyman-limit systems (LLSs) with a column-density distribution slope of βpLLS ∼ -2 are required to explain the data at the low-transmission end of transmission PDF, while uncertainties in the mean Lyα forest transmission affect the high-transmission end. After modeling the LLSs and marginalizing over mean transmission uncertainties, we find that γ = 1.6 best describes the data over our entire redshift range, although constraints on T0 are affected by systematic uncertainties. Within our model framework, isothermal or inverted temperature-density relationships (γ & le; 1) are disfavored at a significance of over 4σ, although this could be somewhat weakened by cosmological and astrophysical uncertainties that we did not model

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Gene Expression Changes Associated with the Airway Wall Response to Injury

Understanding the way in which the airway heals in response to injury is fundamental to dissecting the mechanisms underlying airway disease pathology. As only limited data is available in relation to the in vivo characterisation of the molecular features of repair in the airway we sought to characterise the dynamic changes in gene expression that are associated with the early response to physical injury in the airway wall.We profiled gene expression changes in the airway wall using a large animal model of physical injury comprising bronchial brush biopsy in anaesthetised sheep. The experimental design featured sequential studies in the same animals over the course of a week and yielded data relating to the response at 6 hours, and 1, 3 and 7 days after injury. Notable features of the transcriptional response included the early and sustained preponderance of down-regulated genes associated with angiogenesis and immune cell activation, selection and differentiation. Later features of the response included the up-regulation of cell cycle genes at d1 and d3, and the latter pronounced up-regulation of extracellular matrix-related genes at d3 and d7.It is possible to follow the airway wall response to physical injury in the same animal over the course of time. Transcriptional changes featured coordinate expression of functionally related genes in a reproducible manner both within and between animals. This characterisation will provide a foundation against which to assess the perturbations that accompany airway disease pathologies of comparative relevance