Application of Data Compression Methods to the Redshift-space distortions of the PSCz galaxy catalogue

We apply a spherical harmonic analysis to the Point Source Redshift Survey (PSCz), to compute the real-space galaxy power spectrum and the degree of redshift distortion caused by peculiar velocities. We employ new parameter eigenvector and hierarchical data compression techniques, allowing a much larger number of harmonic modes to be included, and correspondingly smaller error bars. Using 4644 harmonic modes, compressed to 2278, we find that the IRAS redshift-space distortion parameter is $beta = 0.39 pm 0.12$ and the amplitude of galaxy clustering on a scale of $k=0.1 Mpch$ is $Delta_{ m gal}(0.1)=0.42 pm 0.02$. Combining these we find the amplitude of mass perturbations is $Delta_m(0.1)=(0.16pm0.04) Omega_m^{-0.6}$. A preliminary model fitting analysis combining the PSCz amplitudes with the CMB and abundance of clusters yields the cosmological matter density parameter $Omega_m=0.16pm 0.03$, the amplitude of primordial perturbations $Q=(8.4pm 3.8) times 10^{-5}$, and the IRAS bias parameter $b=0.84pm 0.28$

Redshift Distortions and Clustering in the PSCz Survey

We have constrained the redshift-distortion parameter $beta equiv Omega^{0.6}/b$ and the real-space power spectrum of the IRAS PSCz survey using a spherical-harmonic redshift-distortion analysis combined with a data compression method which is designed to deal with correlated parameters. Our latest result, $beta=0.4 pm 0.1$, strongly rules out $beta=1$

Rehabilitation professionals' perceptions of the use of new visualisation software tools with people with stroke

Purpose: Theenvisageprogramme of research was funded to explore and evaluate the use of visualisation software tools using biomechanical data within rehabilitation. Three work packages were developed to evaluate the impact of the tools within stroke rehabilitation. The research presented here aimed at exploring the perceptions of rehabilitation therapists about the use of the visualisation software tools in the context of future randomised controlled trials and stroke rehabilitation practice. Methods: Sixteen therapists working in a range of stroke rehabilitation contexts participated in semi-structured interviews. Interview questions explored their current practice, and the perceived impact of the new visualisation technologies on their workplace environment and practice. Framework analysis was used to analyse the textual data. Results: In general, the stroke therapists were enthusiastic about the potential application of the visualisation software tools. Three themes were identified through qualitative framework analysis: potential uses of the visualisation tools; integration within current service provision; and trial involvement. Conclusions: The study highlights important contextual considerations which may impact significantly on the success of novel technologies in stroke rehabilitation. Normalisation process theory was proposed as a useful process evaluation methodology to optimise both trial evaluation and future service implementation

Evolutionary maintenance of filovirus-like genes in bat genomes

<p>Abstract</p> <p>Background</p> <p>Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genomes and tested for evolutionary maintenance. We also estimated the age of filovirus VP35-like gene integrations and tested the phylogenetic hypotheses that there is a eutherian mammal clade and a marsupial/ebolavirus/Marburgvirus dichotomy for filoviruses.</p> <p>Results</p> <p>We detected homologous copies of VP35-like and NP-like gene integrations in both Old World and New World species of <it>Myotis </it>(bats). We also detected previously unknown VP35-like genes in rodents that are positionally homologous. Comprehensive phylogenetic estimates for filovirus NP-like and VP35-like loci support two main clades with a marsupial and a rodent grouping within the ebolavirus/Lloviu virus/Marburgvirus clade. The concordance of VP35-like, NP-like and mitochondrial gene trees with the expected species tree supports the notion that the copies we examined are orthologs that predate the global spread and radiation of the genus <it>Myotis</it>. Parametric simulations were consistent with selective maintenance for the open reading frame (ORF) of VP35-like genes in <it>Myotis</it>. The ORF of the filovirus-like VP35 gene has been maintained in bat genomes for an estimated 13. 4 MY. ORFs were disrupted for the NP-like genes in <it>Myotis</it>. Likelihood ratio tests revealed that a model that accommodates positive selection is a significantly better fit to the data than a model that does not allow for positive selection for VP35-like sequences. Moreover, site-by-site analysis of selection using two methods indicated at least 25 sites in the VP35-like alignment are under positive selection in <it>Myotis</it>.</p> <p>Conclusions</p> <p>Our results indicate that filovirus-like elements have significance beyond genomic imprints of prior infection. That is, there appears to be, or have been, functionally maintained copies of such genes in mammals. "Living fossils" of filoviruses appear to be selectively maintained in a diverse mammalian genus (<it>Myotis</it>).</p

Virus-host co-evolution under a modified nuclear genetic code

Among eukaryotes with modified nuclear genetic codes, viruses are unknown. However, here we provide evidence of an RNA virus that infects a fungal host (Scheffersomyces segobiensis) with a derived nuclear genetic code where CUG codes for serine. The genomic architecture and phylogeny are consistent with infection by a double-stranded RNA virus of the genus Totivirus. We provide evidence of past or present infection with totiviruses in five species of yeasts with modified genetic codes. All but one of the CUG codons in the viral genome have been eliminated, suggesting that avoidance of the modified codon was important to viral adaptation. Our mass spectroscopy analysis indicates that a congener of the host species has co-opted and expresses a capsid gene from totiviruses as a cellular protein. Viral avoidance of the host’s modified codon and host co-option of a protein from totiviruses suggest that RNA viruses co-evolved with yeasts that underwent a major evolutionary transition from the standard genetic code

Climate-associated tundra thaw pond formation and range expansion of boreal zooplankton predators

© 2015 Nordic Society Oikos. Most of the freshwater component of the Earth's surface is composed of shallow tundra ponds. These high latitude ecosystems have been exposed to a variety of abiotic disturbances associated with recent environmental change. However, the biological significance of these changes remains poorly understood. Here, we characterize the abiotic disturbance to the shallow tundra ponds of northwest Alaska. We used historical aerial imagery to determine that up to 53% of the sampled ponds have formed during the recent warmer decades (since the 1970s). We discovered that two top predator species (phantom midges of the genus Chaoborus) of the freshwater zooplankton have recently undergone range expansion, forming widespread (a scale of hundreds of km) stable tundra populations. We assessed the population persistence of these boreal predators by longitudinal sampling over 14 yr. Recent thaw ponds had significantly dissimilar zooplankton communities to communities of ponds that formed before 1950. Both predator and herbivore species differed by age of pond. Younger pond ages and warmer surface temperatures were the significant predictors of the presence of temperate Chaoborus americanus in tundra ponds. Ponds containing tundra populations of C. americanus and C. cf. flavicans were associated with recent formation (83-90%). Recent ponds in river valleys appeared more important than recent ponds near roads as colonization corridors for C. americanus. Only 24% of the tundra keystone predator, Heterocope septentrionalis, populations were from recent ponds. Our results suggest that climate-associated disturbance can lead to a widespread stable range expansion of boreal species despite the propinquity of older ponds with top-down control exerted by an endemic keystone predator

Cosmological constraints from COMBO-17 using 3D weak lensing

We present the first application of the 3D cosmic shear method developed in Heavens et al. (2006) and the geometric shear-ratio analysis developed in Taylor et al. (2006), to the COMBO-17 data set. 3D cosmic shear has been used to analyse galaxies with redshift estimates from two random COMBO-17 fields covering 0.52 square degrees in total, providing a conditional constraint in the (sigma_8, Omega_m) plane as well as a conditional constraint on the equation of state of dark energy, parameterised by a constant w= p/rho c^2. The (sigma_8, Omega_m) plane analysis constrained the relation between sigma_8 and Omega_m to be sigma_8(Omega_m/0.3)^{0.57 +- 0.19}=1.06 +0.17 -0.16, in agreement with a 2D cosmic shear analysis of COMBO-17. The 3D cosmic shear conditional constraint on w using the two random fields is w=-1.27 +0.64 -0.70. The geometric shear-ratio analysis has been applied to the A901/2 field, which contains three small galaxy clusters. Combining the analysis from the A901/2 field, using the geometric shear-ratio analysis, and the two random fields, using 3D cosmic shear, w is conditionally constrained to w=-1.08 +0.63 -0.58. The errors presented in this paper are shown to agree with Fisher matrix predictions made in Heavens et al. (2006) and Taylor et al. (2006). When these methods are applied to large datasets, as expected soon from surveys such as Pan-STARRS and VST-KIDS, the dark energy equation of state could be constrained to an unprecedented degree of accuracy.Comment: 10 pages, 4 figures. Accepted to MNRA

Density and Velocity Fields from the PSCz Survey

We present the results for the predicted density and peculiar velocity fields and the dipole from the PSCz survey of 15,000 IRAS galaxies over 84% of the sky. We find a significant component to the dipole arising between 6000 and 15,000 km/s, but no significant component from greater distances. The misalignment with the CMB is 20 degrees. The most remarkable feature of the PSCz model velocity field is a coherent large-scale flow along the baseline connecting Perseus-Pisces, the Local Supercluster, Great Attractor and the Shapley Concentration. We have measured the parameter beta using the amplitude of the dipole, bulk flow and point by point comparisons between the individual velocities of galaxies in the MarkIII and SFI datasets, and the large-scale clustering distortion in redshift space.All our results are consistent with beta = 0.6 +- 0.1.Comment: 8 pages, 8 figures. To appear in 'Towards an Understanding of Cosmic Flows', Victoria, July 1999, eds Courteau,S., Strauss,M., Willick,J. PAS