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

Archeops: an instrument for present and future cosmology

Archeops is a balloon-borne instrument dedicated to measure the cosmic microwave background (CMB) temperature anisotropies. It has, in the millimetre domain (from 143 to 545 GHz), a high angular resolution (about 10 arcminutes) in order to constrain high l multipoles, as well as a large sky coverage fraction (30%) in order to minimize the cosmic variance. It has linked, before WMAP, Cobe large angular scales to the first acoustic peak region. From its results, inflation motivated cosmologies are reinforced with a flat Universe (Omega_tot=1 within 3%). The dark energy density and the baryonic density are in very good agreement with other independent estimations based on supernovae measurements and big bang nucleosynthesis. Important results on galactic dust emission polarization and their implications for Planck are also addressed.Comment: 4 pages, 2 figures, to appear in Proceedings of the Multiwavelength Cosmology Conference, June 2003, Mykonos Island, Greec

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

Deuterium at high-redshift: Primordial abundance in the zabs = 2.621 damped Ly-alpha system towards CTQ247

The detection of neutral deuterium in the low-metallicity damped Lyman-{\alpha} system at zabs = 2.621 towards the quasar CTQ247 is reported. Using a high signal-to-noise and high spectral resolution (R = 60000) spectrum from the Very Large Telescope Ultraviolet and Visual Echelle Spectrograph, we precisely measure the deuterium-to-oxygen ratio log N(DI)/N(OI) = 0.74+/-0.04, as well as the overall oxygen abundance, log N(OI)/N(HI)=-5.29+/-0.10 (or equivalently [O/H]=-1.99+/-0.10 with respect to the solar value). Assuming uniform metallicity throughout the system, our measurement translates to (D/H) = (2.8+0.8 -0.6)x10^-5. This ratio is consistent within errors (<0.4sigma) with the primordial ratio, (D/H)p = (2.59+/-0.15)x10^-5, predicted by standard Big-Bang Nucleosynthesis using the WMAP7 value of the cosmological density of baryons (100 Omega_b h^2 = 2.249+/-0.056). The DI absorption lines are observed to be broader than the OI absorption lines. From a consistent fit of the profiles we derive the turbulent broadening to be 5.2 km/s and the temperature of the gas to be T = 8800+/-1500 K, corresponding to a warm neutral medium.Comment: Accepted for publication in A&A Letter

AnnotationBustR: an R package to extract subsequences from GenBank annotations

Background DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively. Results The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses

Script development as a ‘wicked problem’

© 2018 Intellect Ltd Article. Both a process and a set of products, influenced by policy as well as people, and incorporating objective agendas at the same time as subjective experiences, script development is a core practice within the screen industry –yet one that is hard to pin down and, to some extent, define. From an academic research perspective, we might say that script development is a ‘wicked problem’ precisely because of these complex and often contradictory aspects. Following on from a recent Journal of Screenwriting special issue on script development (2017, vol. 8:3), and in particular an article therein dedicated to reviewing the literature and ‘defining the field’, an expanded team of researchers follow up on those ideas and insights. In this article, then, we attempt to theorize script development as a ‘wicked problem’ that spans a range of themes and disciplines. As a ‘wicked’ team of authors, our expertise encompasses screenwriting theory, screenwriting practice, film and television studies, cultural policy, ethnography, gender studies and comedy. By drawing on these critical domains and creative practices, we present a series of interconnected themes that we hope not only suggests the potential for script development as a rich and exciting scholarly pursuit, but that also inspires and encourages other researchers to join forces in an attempt to solve the script development ‘puzzle’

Constraining the variation of the coupling constants with big bang nucleosynthesis

We consider the possibility of the coupling constants of the $SU(3)\times SU(2)\times U(1)$ gauge interactions at the time of big bang nucleosynthesis having taken different values from what we measure at present, and investigate the allowed difference requiring the shift in the coupling constants not violate the successful calculation of the primordial abundances of the light elements. We vary gauge couplings and Yukawa couplings (fermion masses) using a model in which their relative variations are governed by a single scalar field, dilaton, as found in string theory. The results include a limit on the fine structure constant $-6.0\times10^{-4}<\Delta\alpha_{EM}/\alpha_{EM}<1.5\times10^{-4}$, which is two orders stricter than the limit obtained by considering the variation of $\alpha_{EM}$ alone.Comment: 7 page

The Deuterium to Hydrogen Abundance Ratio Towards a Fourth QSO: HS0105+1619

We report the measurement of the primordial D/H abundance ratio towards QSO \object. The column density of the hydrogen in the $z \simeq 2.536$ Lyman limit system is high, \lnhi $= 19.422 \pm 0.009$ \cmm, allowing for the deuterium to be seen in 5 Lyman series transitions. The measured value of the D/H ratio towards QSO \object is found to be D/H$= 2.54 \pm 0.23 \times 10^{-5}$. The metallicity of the system showing D/H is found to be $\simeq 0.01$ solar, indicating that the measured D/H is the primordial D/H within the measurement errors. The gas which shows D/H is neutral, unlike previous D/H systems which were more highly ionized. Thus, the determination of the D/H ratio becomes more secure since we are measuring it in different astrophysical environments, but the error is larger because we now see more dispersion between measurements. Combined with prior measurements of D/H, the best D/H ratio is now D/H$= 3.0 \pm 0.4 \times 10^{-5}$, which is 10% lower than the previous value. The new values for the baryon to photon ratio, and baryonic matter density derived from D/H are $\eta = 5.6 \pm 0.5 \times 10^{-10}$ and \ob $=0.0205 \pm 0.0018$ respectively.Comment: Minor text and reference changes. To appear in the May 10, 2001 issue of the Astrophysical Journa

Antigen receptor repertoires of one of the smallest known vertebrates

The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. “Singkep” (“minifish”). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses