The TOOT Survey: status and early results

The TexOx-1000 (TOOT) radio source redshift survey is designed to find and study typical radio-loud active galaxies to high redshift. They are typical in the same sense that L* galaxies are typical of galaxies in the optical. Previous surveys have only included the most luminous, rare objects at and beyond the peak of activity at z~2, but in going a factor of 100 fainter than the 3C survey, and in assembling a large sample, TOOT probes for the first time the objects that dominate the radio luminosity density of the universe at high redshift. Here we describe the current status of the TOOT survey and draw preliminary conclusions about the redshift distribution of the radio sources. So far, ~520 of the 1000 radio sources have redshifts, with ~440 of those in well-defined, complete, sub-regions of the survey. For these we find a median redshift of z=1, but the measured redshift distribution has a deficit of objects with z~2, when compared to predictions based on extrapolating luminosity functions constrained by higher-flux-density samples. These are the more luminous objects that usually show emission lines, and which should not be missed in the survey unless they are heavily reddened. The deficit may be real, but it would not be too surprising to find a population of faint, reddened radio sources at z~2-3 among the TOOT sources yet to have accurate redshifts.Comment: 6 pages, 2 figures. To appear in the proceedings of the conference "Radio Galaxies: Past, present and future", Leiden, 11-15 Nov 2002, eds. M. Jarvis et a

Determining the cosmic ray ionization rate in dynamically evolving clouds

The ionization fraction is an important factor in determining the chemical and physical evolution of star forming regions. In the dense, dark starless cores of such objects, the ionization rate is dominated by cosmic rays; it is therefore possible to use simple analytic estimators, based on the relative abundances of different molecular tracers, to determine the cosmic ray ionization rate. This paper uses a simple model to investigate the accuracy of two well-known estimators in dynamically evolving molecular clouds. It is found that, although the analytical formulae based on the abundances of H3+,H2,CO,O,H2O and HCO+ give a reasonably accurate measure of the cosmic ray ionization rate in static, quiescent clouds, significant discrepancies occur in rapidly evolving (collapsing) clouds. As recent evidence suggests that molecular clouds may consist of complex, dynamically evolving sub-structure, we conclude that simple abundance ratios do not provide reliable estimates of the cosmic ray ionization rate in dynamically active regions.Comment: Accepted by A&A. 17 pages, 4 figure

Dis-locations and Broken Narratives: articulating liminal and interstitial experiences through a series of moving image and mixed media installations

This practice led research explores three video and mixed media artworks created and exhibited between 2006-17. Mariners and Migrants: in Search of Home, (2006) WAVE/ING, (2011/12) and Dear Child, (2016/7) are part of a substantive body of artwork which has been produced since the late discovery of my adoption in 1991. This event and its effect changed both the content and shape of my work reflecting my personal response to the experience of otherness and dis-location identified as, “The feeling of being between places and people, the sense of transience, the experience of seeing the world and one’s place in it from different perspectives.” 1 This led to the creation of multi-layered artworks inspired by narratives of migration and exile and the the development of various imagistic and material strategies which reflect liminality. These include acausal2, non-linear editing and asynchronous multi channel projections and layers of glass and silk within expanded installations. The three main sections of this commentary relate to different elements of the research journey. They cover responses to historic events and narratives, the distinctive use of original archives, the function of physical journeys in the development and making of artworks and the use of interpretive dance to create an embodied response to loss. I would argue that my situated and exploratory practice, applied throughout the development and production process was effective in transforming the effects of dissociation and dissonance3 into innovative imagistic outcomes. This is situated in relation to other artists working with trauma and memory and to key ideas around post adoptive psychology with reference to other feminist theorists. This body of work represents an effective and fluid response to the dis-locations of late discovery which is not principally therapeutic or sociological in intent

The MEROPS Database

Many proteins undergo important post-translational proteolytic processing to remove targeting signals and activation peptides, and most proteins undergo proteolytic inactivation and catabolism. The enzymes that hydrolyse the peptide bonds in proteins and peptides are known as peptidases, proteases or proteolytic enzymes. The MEROPS database ("http://merops.sanger.ac.uk":http://merops.sanger.ac.uk) presents the classification and nomenclature of peptidases, their inhibitors and substrates. In 1993 we proposed the scheme for the classification of peptidases that has been internationally accepted, and in 1996 we established the MEROPS database. Protein inhibitors have been included in the database since 2004. About 2% of the genes in a genome encode peptidase homologues, and a further 1% encode protein inhibitors. For example, the human genome has 1037 genes encoding peptidase homologues (of which 643 are known or predicted to be active peptidases) and 433 protein inhibitor genes (of which 144 have been biochemically characterized as inhibitors). 

The MEROPS classification is hierarchical. Sequences are grouped into a peptidase species (each of which is given a unique identifier, for example C01.060 for cathepsin B); peptidase species are grouped into a family (for example C1); and families grouped into a clan (for example CA). To be included in the same protein species, sequences must be derived from the same node on a dendrogram derived from the family sequence alignment and known (or predicted) to share similar specificity. To be included in the same family sequences must be homologous over the sequence domain that contains the active site residues (peptidases) or reactive site (inhibitors). To be included in the same clan, the proteins must share similar tertiary structures (or the same linear arrangement of active site residues if the structure is unknown). Over 117,000 peptidase homologues are classified into 3114 protein species, 205 families and 52 clans, and 12,104 protein inhibitors are classified into 663 protein species, 64 families and 33 clans.

The database includes manually curated summaries for each clan, family and protein species. There are also sequence alignments and manually curated bibliographies (with over 41,000 references) at every level. In addition to protein inhibitors we also include 158 manually curated summaries for synthetic and naturally occurring small molecule inhibitors. There is also a summary page for each organism listing all known homologues and an analysis highlighting significant presences, absences or gene family expansions for organisms with a completely sequenced genome. 

The MEROPS database includes known peptidase substrates: naturally occurring peptides and proteins, and synthetic substrates. Currently there are 4091 cleavages of synthetic substrates and 95,413 cleavages of proteins (of which 74,740 are physiological). Cleavages in proteins are mapped to UniProt entries. An alignment of very close homologues of each substrate sequence is shown, highlighting residues around each cleavage site indicating whether the peptidase is known to accept the amino acid at that position or not. Cleavage sites that are conserved are likely to be physiological; cleavage sites that are not conserved may be pathological for the species in which they occur or coincidental.

The MEROPS data is freely available to download from our FTP site ("http://ftp.sanger.ac.uk/pub/MEROPS":http://ftp.sanger.ac.uk/pub/MEROPS) and via our Distributed Annotation System (DAS) server ("http://das.sanger.ac.uk/das/merops":http://das.sanger.ac.uk/das/merops).
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Extremely red galaxy counterparts to 7C radio sources

We present RIJHK imaging of seven radio galaxies from the 7C Redshift Survey (7CRS) which lack strong emission lines and we use these data to investigate their spectral energy distributions (SEDs) with models which constrain their redshifts. Six of these seven galaxies have extremely red colours (R-K>5.5) and we find that almost all of them lie in the redshift range 1<z<2. We also present near-infrared spectroscopy of these galaxies which demonstrate that their SEDs are not dominated by emission lines, although tentative lines, consistent with H-alpha at z=1.45 and z=1.61, are found in two objects. Although the red colours of the 7CRS galaxies can formally be explained by stellar populations which are either very old or young and heavily reddened, independent evidence favours the former hypothesis. At z~1.5 at least 1/4 of powerful radio jets are triggered in massive (>L*) galaxies which formed the bulk of their stars several Gyr earlier, that is at epochs corresponding to redshifts z>5. If a similar fraction of all z~1.5 radio galaxies are old, then extrapolation of the radio luminosity function shows that, depending on the radio source lifetimes, between 10-100% of the near-IR selected extremely red object (ERO) population undergo a radio outburst at epochs corresponding to 1<z<2. An ERO found serendipitously in the field of one of the 7CRS radio sources appears to be a radio-quiet analogue of the 7CRS EROs with an emission line likely to be [OII] at z=1.20. The implication is that some of the most massive elliptical galaxies formed the bulk of their stars at z>5 and these objects probably undergo at least two periods of AGN activity: one at high redshift during which the black hole forms and another one at an epoch corresponding to z~1.5.Comment: 20 pages, 10 figures, accepted for publication in MNRA

The Nature and Evolution of Classical Double Radio Sources from Complete Samples

We present a study of the trends in luminosity, linear size, spectral index, and redshift of classical double radio sources from three complete samples selected at successively fainter low radio-frequency flux-limits. We have been able to decouple the effects of the tight correlation between redshift and luminosity (inherent in any single flux-limited sample) which have hitherto hindered interpretation of the relationships between these four source properties. The major trends found are that (i) spectral indices increase with linear size, (ii) rest-frame spectral indices have a stronger dependence on luminosity than on redshift except at high (GHz) frequencies, and that (iii) the linear sizes are smaller at higher redshifts. We reproduce the observed dependences in a model for radio sources (born throughout cosmic time according to a radio-source birth function) whose lobes are fed with a synchrotron-emitting population (whose energy distribution is governed by compact hotspots), and which suffer inverse Compton, synchrotron and adiabatic expansion losses. In simulating the basic observed dependences, we find that there is no need to invoke any systematic change in the environments of these objects with redshift if the consequences of imposing a survey flux-limit on our simulated datasets are properly included in the model. We present evidence that for a radio survey there is an unavoidable `youth--redshift degeneracy', even though radio sources are short-lived relative to the age of the Universe; it is imperative to take this into account in studies which seemingly reveal correlations of source properties with redshift such as the `alignment effect'.Comment: 48 pages, 19 figures, uses aas2pp4.sty. To appear in AJ. Also available at http://www-astro.physics.ox.ac.uk/~kmb References updated and minor typos correcte

Time and M-theory

We review our recent proposal for a background independent formulation of a holographic theory of quantum gravity. The present review incorporates the necessary background material on geometry of canonical quantum theory, holography and spacetime thermodynamics, Matrix theory, as well as our specific proposal for a dynamical theory of geometric quantum mechanics, as applied to Matrix theory. At the heart of this review is a new analysis of the conceptual problem of time and the closely related and phenomenologically relevant problem of vacuum energy in quantum gravity. We also present a discussion of some observational implications of this new viewpoint on the problem of vacuum energy.Comment: 86 pages, 5 figures, LaTeX, typos fixed, references added, and Sec. 6.2 revised; invited review for Int. J. Mod. Phys.

Oscillations in the stable starless core Barnard 68

New molecular line observations of the Bok globule Barnard 68 in HCO+ irrefutably confirm the complex pattern of red and blue asymmetric line profiles seen across the face of the cloud in previous observations of CS. The new observations thus strengthen the previous interpretation that Barnard 68 is undergoing peculiar oscillations. Furthermore, the physical chemistry of B68 indicates that the object is much older than the sound crossing time and is therefore long-lived. A model is presented for the globule in which a modest external pressure perturbation is shown to lead to oscillations about a stable equilibrium configuration. Such oscillations may be present in other stable starless cores as manifested by a similar signature of inward and outward motions.Comment: Accepted for MNRAS letters, 5 pages, 7 figure

The 6C** Sample and the Highest Redshift Radio Galaxies

We present a new radio sample, 6C** designed to find radio galaxies at z > 4 and discuss some of its near-infrared imaging follow-up results.Comment: 2 pages, 2 figures, to appear in proceedings of 'Multi-wavelength AGN surveys', Cozumel, 200