Signal-to-noise ratios, instrument parameters and repeatability of Itrax XRF core scan measurements of floodplain sediments

This study used signal-to-noise ratios to assess the effects of increasing Itrax XRF instrument parameters, namely tube voltage, tube current and exposure time, on XRF spectra and measurement repeatability. Tests were performed on cores from British and Irish floodplains. Seven combinations of tube voltage and current and six exposure times were compared using signal-to-noise ratios for eight target elements. Signal-to-noise ratios may be substantially improved by selecting instrument parameters, particularly tube voltage, for specific target elements. They can also be used to assess element profile suitability for interpretation by comparison with the limit of quantification. Repeatability was assessed using the standard deviation of measurements in nine repeat scans. The variation in element levels in the majority of profiles is considerably greater than the variability in individual measurements

Prograde and Retrograde Black Holes: Whose Jet is More Powerful?

The outflow efficiency (eta) from black hole (BH) accretion disc systems is known to depend upon both the BH spin (a) and the amount of large-scale magnetic flux threading the BH and disc. Semi-analytical flux-trapping models suggest retrograde BHs should trap much more large-scale magnetic flux near the BH leading to much higher eta than for prograde BHs. We self-consistently determine the amount of large-scale magnetic flux trapped by rapidly spinning (a = -0.9 and 0.9) BHs using global 3D time-dependent non-radiative general relativistic magnetohydrodynamic simulations of thick (h/r ~ 0.3-0.6) discs. We find that BH-trapped flux builds up until it is strong enough to disrupt the inner accretion disc. Contrary to prior flux-trapping models, which do not include the back-reaction of magnetic flux on the disc, our simulations show prograde BHs trap more magnetic flux, leading to about 3 times higher eta than retrograde BHs for |a| = 0.9. Both spin orientations can produce highly efficient jets, eta ~ 100%, with increasing eta for increasing disc thickness. The similarity of eta for prograde and retrograde BHs makes it challenging to infer the sign of BH spin based on jet energetics alone.Comment: 5 pages, 3 figures. Accepted to MNRAS. For associated movies see http://youtu.be/yNZLjsrz0Wo and http://youtu.be/bQE69wti3a

Ontological dependence in a spacetime-world

Priority Monism (hereafter, ‘Monism’), as defined by Jonathan Schaffer (Philos Rev 119:131–176, 2010), has a number of components. It is the view that: the cosmos exists; the cosmos is a maximal actual concrete object, of which all actual concrete objects are parts; the cosmos is basic—there is no object upon which the cosmos depends, ontologically; ontological dependence is a primitive and unanalysable relation. In a recent attack, Lowe (Spinoza on monism. Palgave Macmillan, London, pp 92–122, 2012) has offered a series of arguments to show that Monism fails. He offers up four tranches of argument, with different focuses. These focal points are: (1) being a concrete object; (2) aggregation and dependence; (3) analyses of ontological dependence; (4) Schaffer’s no-overlap principle. These are all technical notions, but each figures at the heart of a cluster of arguments that Lowe puts forward. To respond, I work through each tranche of argument in turn. Before that, in the first section, I offer a cursory statement of Monism, as Schaffer presents it in his 2010 paper, Monism: The Priority of the Whole. I then respond to each of Lowe’s criticisms in turn, deploying material from Schaffer’s 2009 paper Spacetime: the One Substance, as well as various pieces of conceptual machinery from Lowe’s own works (The possibility of metaphysics. Clarendon, Oxford, 1998, 2010) to deflect Lowe’s (Spinoza on monism. Palgave Macmillan, London, pp 92–122, 2012) attacks. In the process of defending Monism from Lowe (Spinoza on monism. Palgave Macmillan, London, pp 92–122, 2012), I end up offering some subtle refinements to Schaffer’s (Philos Rev 119:131–176, 2010) view and explain how the resulting ‘hybrid’ view fares in the wider dialectic

Graduate Recital: Jonathan Daly

Kemp Recital HallApril 15, 2013Monday Evening6:30 p.m

Immodest and proud

In his ‘Ambitious, Yet Modest, Metaphysics’, Hofweber (Metametaphysics, Oxford University Press, Oxford, pp 260–289, 2009a) puts forward arguments against positions in metaphysics that he describes as ‘immodest’; a position he identifies as defended by Jonathan Lowe. In this paper I reply to Hofweber’s arguments, offering a defence of immodest metaphysics of the type practiced by Lowe (The possibility of metaphysics, Oxford University Press, Oxford, 1998) inter alia

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.This work was supported by Wellcome Trust WT091501MAThis is the author accepted manuscript. It is currently under an indefinite embargo pending publication by PLOS

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations