A fourth HI 21-cm absorption system in the sight-line of MG J0414+0534: a record for intervening absorbers

We report the detection of a strong HI 21-cm absorption system at z=0.5344, as well as a candidate system at z=0.3389, in the sight-line towards the z=2.64 quasar MG J0414+0534. This, in addition to the absorption at the host redshift and the other two intervening absorbers, takes the total to four (possibly five). The previous maximum number of 21-cm absorbers detected along a single sight-line is two and so we suspect that this number of gas-rich absorbers is in some way related to the very red colour of the background source. Despite this, no molecular gas (through OH absorption) has yet been detected at any of the 21-cm redshifts, although, from the population of 21-cm absorbers as a whole, there is evidence for a weak correlation between the atomic line strength and the optical--near-infrared colour. In either case, the fact that so many gas-rich galaxies (likely to be damped Lyman-alpha absorption systems) have been found along a single sight-line towards a highly obscured source may have far reaching implications for the population of faint galaxies not detected in optical surveys, a possibility which could be addressed through future wide-field absorption line surveys with the Square Kilometre Array.Comment: Accepted by ApJ Letter

HI and OH absorption in the lensing galaxy of MG J0414+0534

We report the detection of \HI 21-cm absorption in the $z=0.96$ early-type lensing galaxy towards MG J0414+0534 with the Green Bank Telescope. The absorption, with total $N_{\rm HI}=1.6 \times 10^{18} (T_{\rm s}/f) {\rm cm}^{-2}$, is resolved into two strong components, probably due to the two strongest lens components, which are separated by 0.4\arcsec. Unlike the other three lenses which have been detected in \HI, J0414+0534 does not exhibit strong OH absorption, giving a OH/\HI column density ratio of N_{\rm OH}/N_{\rm HI}\lapp10^{-6} (for $T_{\rm s}=100$ K, $T_{\rm x}=10$ K and $f_{\rm HI}=f_{\rm OH}=1$). This underabundance of molecular gas may indicate that the extreme optical--near-IR colour ($V-K=10.26$) along the line-of-sight is not due to the lens. We therefore suggest that despite the strong upper limits on molecular absorption at the quasar redshift, as traced by millimetre lines, the extinction occurs primarily in the quasar host galaxy.Comment: Accepted by MNRAS Letters, 5 (and a bit) pages, 5 figure

Further Observational Evidence for a Critical Ionising Luminosity in Active Galaxies

We report the results of a survey for HI 21-cm absorption at redshifts of z > 2.6 in a new sample of radio sources with the Green Bank and Giant Metrewave Radio Telescopes. From a total of 25 targets, we report zero detections in the 16 for which optical depth limits could be obtained. Based upon the detection rate for z > 0.1 associated absorption, we would expect approximately four detections. Of the 11 which have previously not been searched, there is sufficient source-frame optical/ultra-violet photometry to determine the ionising photon rate for four. Adding these to the literature, the hypothesis that there is a critical rate of logQ = 56 ionising photons per second is now significant at ~7 sigma. This reaffirms our assertion that searching z > 3 active galaxies for which optical redshifts are available selects sources in which the ultra-violet luminosity is sufficient to ionise all of the neutral gas in the host galaxy.Comment: Accepted by MNRA

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn from a high-throughput sequencing experiment. Here, the self-similar distributions appear as part of the evaluation of the error rate of the sequencing technology and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in electronic clinical data. The distributions are also relevant to identification of subclonal populations in tumors and the study of the evolution of infectious diseases, and more precisely the study of quasi-species and intrahost diversity of viral populations

Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. The process has parallels with paper folding sequences that arise when a piece of paper is folded several times and then unfolded. Here we adapt such methods to study the breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are 2^(n(n-1)/2) qualitatively distinct evolutions involving n breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the fold positions, to determine evolution likelihoods, and also describe how amplicons become localised. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples

Statistical model-based testing to evaluate the recurrence of genomic aberrations

Motivation: In cancer genomes, chromosomal regions harboring cancer genes are often subjected to genomic aberrations like copy number alteration and loss of heterozygosity. Given this, finding recurrent genomic aberrations is considered an apt approach for screening cancer genes. Although several permutation-based tests have been proposed for this purpose, none of them are designed to find recurrent aberrations from the genomic dataset without paired normal sample controls. Their application to unpaired genomic data may lead to false discoveries, because they retrieve pseudo-aberrations that exist in normal genomes as polymorphisms

How to humiliate and shame: A reporter's guide to the power of the mugshot

This is an Author's Accepted Manuscript of an article published in Social Semiotics, 24(1), 56-87, 2014, copyright Taylor & Francis, available online at: http://www.tandfonline.com/The judicial photograph – the “mugshot” – is a ubiquitous and instantly recognisable form, appearing in the news media, on the internet, on book covers, law enforcement noticeboards and in many other mediums. This essay attempts to situate the mugshot in a historical and theoretical context to explain the explicit and implicit meaning of the genre as it has developed, focussing in particular on their use in the UK media in late modernity. The analysis is based on the author's reflexive practice as a journalist covering crime in the national news media for 30 years and who has used mugshots to illustrate stories for their explicit and specific content. The author argues that the visual limitations of the standardised “head and shoulders” format of the mugshot make it a robust subject for analysing the changing meaning of images over time. With little variation in the image format, arguments for certain accreted layers of signification are easier to make. Within a few years of the first appearance of the mugshot form in the mid-19th century, it was adopted and adapted as a research tool by scientists and criminologists. While the positivist scientists claimed empirical objectivity we can now see that mugshots played a part in the construction of subjective notions of “the other”, “the lesser” or “sub-human” on the grounds of class, race and religion. These dehumanising ideas later informed the theorists and bureaucrats of National Socialist ideology from the 1920s to 1940s. The author concludes that once again the mugshot has become, in certain parts of the media, a signifier widely used to exclude or deride certain groups. In late modernity, the part of the media that most use mugshots – the tabloid press and increasingly tabloid TV – is part of a neo-liberal process that, in a conscious commercial appeal to the paying audience, seeks to separate rather than unify wider society