Relative Flux Calibration of Keck HIRES Echelle Spectra

We describe a new method to calibrate the relative flux levels in spectra from the HIRES echelle spectrograph on the Keck-I telescope. Standard data reduction techniques that transfer the instrument response between HIRES integrations leave errors in the flux of 5 - 10%, because the effective response varies. The flux errors are most severe near the ends of each spectral order, where there can be discontinuous jumps. The source of these errors is uncertain, but may include changes in the vignetting connected to the optical alignment. Our new flux calibration method uses a calibrated reference spectrum of each target to calibrate individual HIRES integrations. We determine the instrument response independently for each integration, and hence we avoid the need to transfer the instrument response between HIRES integrations. The procedure can be applied to any HIRES spectrum, or any other spectrum. While the accuracy of the method depends upon many factors, we have been able to flux calibrate a HIRES spectrum to 1% over scales of 200 A that include order joins. We illustrate the method with spectra of Q1243+3047 towards which we have measured the deuterium to hydrogen abundance ratio.Comment: 24 pages, 17 figures, submitted to PAS

Predicting QSO Continua in the Ly Alpha Forest

We present a method to make predictions with sets of correlated data values, in this case QSO flux spectra. We predict the continuum in the Lyman-Alpha forest of a QSO, from 1020 -- 1216 A, using the spectrum of that QSO from 1216 -- 1600 A . We find correlations between the unabsorbed flux in these two wavelengths regions in the HST spectra of 50 QSOs. We use principal component analysis (PCA) to summarize the variety of these spectra and we relate the weights of the principal components for 1020 -- 1600 A to the weights for 1216 -- 1600 A, and we apply this relation to make predictions. We test the method on the HST spectra, and we find an average absolute flux error of 9%, with a range 3 -- 30%, where individual predictions are systematically too low or too high. We mention several ways in which the predictions might be improved.Comment: 17 pages, 4 figures, submitted to Ap

The Keck+Magellan Survey for Lyman Limit Absorption II: A Case Study on Metallicity Variations

We present an absorption line analysis of the Lyman limit system (LLS) at z=3.55 in our Magellan/MIKE spectrum of PKS2000-330. Our analysis of the Lyman limit and full HI Lyman series constrains the total HI column density of the LLS (N_HI = 10^[18.0 +/- 0.25] cm^{-2} for b_HI >= 20 km/s) and also the N_HI values of the velocity subsystems comprising the absorber. We measure ionic column densities for metal-line transitions associated with the subsystems and use these values to constrain the ionization state (>90% ionized) and relative abundances of the gas. We find an order of magnitude dispersion in the metallicities of the subsystems, marking the first detailed analysis of metallicity variations in an optically thick absorber. The results indicate that metals are not well mixed within the gas surrounding high $z$ galaxies. Assuming a single-phase photoionization model, we also derive an N_H-weighted metallicity, = -1.66 +/- 0.25, which matches the mean metallicity in the neutral ISM in high z damped Lya systems (DLAs). Because the line density of LLSs is ~10 times higher than the DLAs, we propose that the former dominate the metal mass-density at z~3 and that these metals reside in the galaxy/IGM interface. Considerations of a multi-phase model do not qualitatively change these conclusions. Finally, we comment on an anomalously large O^0/Si^+ ratio in the LLS that suggests an ionizing radiation field dominated by soft UV sources (e.g. a starburst galaxy). Additional abundance analysis is performed on the super-LLS systems at z=3.19.Comment: 20 pages, 7 figures (most in color). Accepted to Ap

A Direct Measurement of the IGM Opacity to HI Ionizing Photons

We present a new method to directly measure the opacity from HI Lyman limit (LL) absorption k_LL along quasar sightlines by the intergalactic medium (IGM). The approach analyzes the average (``stacked'') spectrum of an ensemble of quasars at a common redshift to infer the mean free path (MFP) to ionizing radiation. We apply this technique to 1800 quasars at z=3.50-4.34 drawn from the Sloan Digital Sky Survey (SDSS), giving the most precise measurements on k_LL at any redshift. From z=3.6 to 4.3, the opacity increases steadily as expected and is well parameterized by MFP = (48.4 +/- 2.1) - (38.0 +/- 5.3)*(z-3.6) h^-1 Mpc (proper distance). The relatively high MFP values indicate that the incidence of systems which dominate k_LL evolves less strongly at z>3 than that of the Lya forest. We infer a mean free path three times higher than some previous estimates, a result which has important implications for the photo-ionization rate derived from the emissivity of star forming galaxies and quasars. Finally, our analysis reveals a previously unreported, systematic bias in the SDSS quasar sample related to the survey's color targeting criteria. This bias potentially affects all z~3 IGM studies using the SDSS database.Comment: 7 pages, 4 figures; Accepted to ApJ

QSO 0130-4021: A third QSO showing a low Deuterium to Hydrogen Abundance Ratio

We have discovered a third quasar absorption system which is consistent with a low deuterium to hydrogen abundance ratio, D/H = 3.4 times 10^-5. The z ~ 2.8 partial Lyman limit system towards QSO 0130-4021 provides the strongest evidence to date against large D/H ratios because the H I absorption, which consists of a single high column density component with unsaturated high order Lyman series lines, is readily modeled -- a task which is more complex in other D/H systems. We have obtained twenty-two hours of spectra from the HIRES spectrograph on the W.M. Keck telescope, which allow a detailed description of the Hydrogen. We see excess absorption on the blue wing of the H I Lyman alpha line, near the expected position of Deuterium. However, we find that Deuterium cannot explain all of the excess absorption, and hence there must be contamination by additional absorption, probably H I. This extra H I can account for most or all of the absorption at the D position, and hence D/H = 0 is allowed. We find an upper limit of D/H < 6.7 times 10^-5 in this system, consistent with the value of D/H ~ 3.4 times 10^-5 deduced towards QSO 1009+2956 and QSO 1937-1009 by Burles and Tytler (1998a, 1998b). This absorption system shows only weak metal line absorption, and we estimate [Si/H] < -2.6 -- indicating that the D/H ratio of the system is likely primordial. All four of the known high redshift absorption line systems simple enough to provide useful limits on D are consistent with D/H = 3.4 +/- 0.25 times 10^-5. Conversely, this QSO provides the third case which is inconsistent with much larger values.Comment: 18 pages, 5 figures, submitted to Ap

Effect of water-to-feed ratio on feed disappearance, growth rate, feed efficiency, and carcass traits in growing-finishing pigs

peer-reviewedThe optimum proportion of water for preparing liquid feed to maximize growth and optimize feed efficiency (FE) in growing-finishing pigs is not known. The aim of the current study was, using an automatic short-trough sensor liquid feeding system, to identify the water-to-feed ratio at which growth was maximized and feed was most efficiently converted to live-weight. Two experiments were conducted in which four commercially used water-to-feed ratios were fed: 2.4:1, 3.0:1, 3.5:1, and 4.1:1 on a dry matter (DM) basis (the equivalent of 2:1, 2.5:1, 3.0:1, and 3.5:1 on a fresh matter basis). Each experiment comprised 216 pigs, penned in groups of 6 same sex (entire male and female) pigs/pen with a total of 9 pen replicates per treatment. The first experiment lasted 62 days (from 40.6 to 102.2 kg at slaughter) and the second experiment was for 76 days (from 31.8 to 119.6 kg at slaughter). Overall, in Exp. 1, FE was 0.421, 0.420, 0.453, and 0.448 (s.e. 0.0081 g/g; P < 0.01) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. Overall, in Exp. 2, average daily gain was 1,233, 1,206, 1,211, and 1,177 (s.e. 12.7 g/day; P < 0.05) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. At slaughter, in Exp. 1, dressing percentage was 76.7, 76.6, 76.7, and 75.8 (s.e. 0.17%; P < 0.01) for 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. There were no differences between treatment groups for DM, organic matter, nitrogen, gross energy, or ash digestibilities. These findings indicate that liquid feeding a diet prepared at a water-to-feed ratio of 3.5:1 maximizes FE of growing-finishing pigs without negatively affecting dressing percentage. Therefore, preparing liquid feed for growing-finishing pigs at a water-to-feed ratio of 3.5:1 DM is our recommendation for a short-trough liquid feeding system

The Keck+Magellan Survey for Lyman Limit Absorption I: The Frequency Distribution of Super Lyman Limit Systems

We present the results of a survey for super Lyman limit systems (SLLS; defined to be absorbers with 19.0 <= log(NHI) <= 20.3 cm^-2) from a large sample of high resolution spectra acquired using the Keck and Magellan telescopes. Specifically, we present 47 new SLLS from 113 QSO sightlines. We focus on the neutral hydrogen frequency distribution f(N,X) of the SLLS and its moments, and compare these results with the Lyman-alpha forest and the damped Lyman alpha systems (DLA; absorbers with log(NHI) >= 20.3 cm^-2). We find that that f(N,X) of the SLLS can be reasonably described with a power-law of index alpha = -1.43^{+0.15}_{-0.16} or alpha = -1.19^{+0.20}_{-0.21} depending on whether we set the lower N(HI) bound for the analysis at 10^{19.0} cm^-2 or 10^{19.3}$ cm^-2, respectively. The results indicate a flattening in the slope of f(N,X) between the SLLS and DLA. We find little evidence for redshift evolution in the shape of f(N,X) for the SLLS over the redshift range of the sample 1.68 < z < 4.47 and only tentative evidence for evolution in the zeroth moment of f(N,X), the line density l_lls(X). We introduce the observable distribution function O(N,X) and its moment, which elucidates comparisons of HI absorbers from the Lyman-alpha through to the DLA. We find that a simple three parameter function can fit O(N,X) over the range 17.0 <= log(NHI) <=22.0. We use these results to predict that f(N,X) must show two additional inflections below the SLLS regime to match the observed f(N,X) distribution of the Lyman-alpha forest. Finally, we demonstrate that SLLS contribute a minor fraction (~15%) of the universe's hydrogen atoms and, therefore, an even small fraction of the mass in predominantly neutral gas.Comment: 15 pages, 10 figures, accepted to the Astrophysical Journal. Revision includes updated reference

PREDOMINANTLY LOW METALLICITIES MEASURED IN A STRATIFIED SAMPLE OF LYMAN LIMIT SYSTEMS AT Z = 3.7

We measured metallicities for 33 z = 3.4–4.2 absorption line systems drawn from a sample of H i-selected-Lyman limit systems (LLSs) identified in Sloan Digital Sky Survey (SDSS) quasar spectra and stratified based on metal line features. We obtained higher-resolution spectra with the Keck Echellette Spectrograph and Imager, selecting targets according to our stratification scheme in an effort to fully sample the LLS population metallicity distribution. We established a plausible range of H i column densities and measured column densities (or limits) for ions of carbon, silicon, and aluminum, finding ionization-corrected metallicities or upper limits. Interestingly, our ionization models were better constrained with enhanced α-to-aluminum abundances, with a median abundance ratio of [α/Al] = 0.3. Measured metallicities were generally low, ranging from [M/H] = −3 to −1.68, with even lower metallicities likely for some systems with upper limits. Using survival statistics to incorporate limits, we constructed the cumulative distribution function (CDF) for LLS metallicities. Recent models of galaxy evolution propose that galaxies replenish their gas from the low-metallicity intergalactic medium (IGM) via high-density H i "flows" and eject enriched interstellar gas via outflows. Thus, there has been some expectation that LLSs at the peak of cosmic star formation (z ≈ 3) might have a bimodal metallicity distribution. We modeled our CDF as a mix of two Gaussian distributions, one reflecting the metallicity of the IGM and the other representative of the interstellar medium of star-forming galaxies. This bimodal distribution yielded a poor fit. A single Gaussian distribution better represented the sample with a low mean metallicity of [M/H] ≈ −2.5.Massachusetts Institute of Technology. Undergraduate Research Opportunities ProgramNational Science Foundation (U.S.) (Award AST-1109915

The HST/ACS+WFC3 Survey for Lyman Limit Systems II: Science

We present the first science results from our Hubble Space Telescope Survey for Lyman limit absorption systems (LLS) using the low dispersion spectroscopic modes of the Advanced Camera for Surveys and the Wide Field Camera 3. Through an analysis of 71 quasars, we determine the incidence frequency of LLS per unit redshift and per unit path length, l(z) and l(x) respectively, over the redshift range 1 < z< 2.6, and find a weighted mean of l(x)=0.29 +/-0.05 for 2.0 < z < 2.5 through a joint analysis of our sample and that of Ribaudo et al. (2011). Through stacked spectrum analysis, we determine a median (mean) value of the mean free path to ionizing radiation at z=2.4 of lambda_mfp = 243(252)h^(-1) Mpc, with an error on the mean value of +/- 43h^(-1) Mpc. We also re-evaluate the estimates of lambda_mfp from Prochaska et al. (2009) and place constraints on the evolution of lambda_mfp with redshift, including an estimate of the "breakthrough" redshift of z = 1.6. Consistent with results at higher z, we find that a significant fraction of the opacity for absorption of ionizing photons comes from systems with N_HI <= 10^{17.5} cm^(-2) with a value for the total Lyman opacity of tau_lyman = 0.40 +/- 0.15. Finally, we determine that at minimum, a 5-parameter (4 power-law) model is needed to describe the column density distribution function f(N_HI, X) at z \sim 2.4, find that f(N_HI,X) undergoes no significant change in shape between z \sim 2.4 and z \sim 3.7, and provide our best fit model for f(N_HI,X).Comment: 36 pages, 20 figures, 10 tables, revision to match accepted ApJ versio

Development and characterisation of a novel three-dimensional inter-kingdom wound biofilm model

Chronic diabetic foot ulcers are frequently colonised and infected by polymicrobial biofilms that ultimately prevent healing. This study aimed to create a novel in vitro inter-kingdom wound biofilm model on complex hydrogel-based cellulose substrata to test commonly used topical wound treatments. Inter-kingdom triadic biofilms composed of Candida albicans, Pseudomonas aeruginosa, and Staphylococcus aureus were shown to be quantitatively greater in this model compared to a simple substratum when assessed by conventional culture, metabolic dye and live dead qPCR. These biofilms were both structurally complex and compositionally dynamic in response to topical therapy, so when treated with either chlorhexidine or povidone iodine, principal component analysis revealed that the 3-D cellulose model was minimally impacted compared to the simple substratum model. This study highlights the importance of biofilm substratum and inclusion of relevant polymicrobial and inter-kingdom components, as these impact penetration and efficacy of topical antiseptics