G/G Models and W_N strings

We derive the BRST cohomology of the G/G topological model for the case of A^{(1)}_{N-1} . It is shown that at level k={p/q}-N the latter describes the (p,q) W_N minimal model coupled to $W_N$ gravity (plus some extra ``topological sectors").Comment: 17 page

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

AbstractHomoplasic single nucleotide polymorphisms (SNPs) are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large WGS datasets (&gt;1,000 isolates and/or &gt;100,000 SNPs). SNPPar takes as input a SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution.Testing on simulated data (120Mycobacterium tuberculosisalignments representing local and global samples) showed SNPPar can detect homoplasic SNPs with very high sensitivity (zero false-positives in all tests) and high specificity (zero false-negatives in 89% of tests). SNPPar analysis of three empirically sampled datasets (E. anophelis, B. dolosaandM. tuberculosis) produced results that were in concordance with previous studies, in terms of both individual homoplasies and evidence of convergence at the codon and gene levels. SNPPar analysis of a simulated alignment of ∼64,000 genome-wide SNPs from 2000M. tuberculosisgenomes took ∼23 minutes and ∼2.6 GB of RAM to generate complete annotated results on a laptop. This analysis required ASR be conducted for only 1.25% of SNPs, and the ASR step took ∼23 seconds and 0.4 GB RAM.SNPPar automates the detection and annotation of homoplasic SNPs efficiently and accurately from large SNP alignments. As demonstrated by the examples included here, this information can be readily used to explore the role of homoplasy in parallel and/or convergent evolution at the level of nucleotide, codon and/or gene.Impact statementDNA sequences of bacterial pathogens are mutating all the time; most changes are deleterious or neutral, but sometimes a mutation leads to functional change that allows the pathogen to evade a potential threat. These random mutational changes (single nucleotide polymorphisms, or SNPs) are so very rarely beneficial, that when they do arise in parallel in distantly related isolates (known as homoplasic SNPs) this indicates that the change may be positively selected because it confers an adaptive advantage to the bacteria.Finding homoplasic SNPs in large sets of bacterial genomes is challenging as current tools require substantial time and computational resources to run. Here we present SNPPar, a software program to efficiently and accurately automate the detection and annotation of homoplasic SNPs from large whole-genome sequence data sets. We use simulated data to demonstrate accuracy of the program, and re-analyse published datasets using SNPPar to illustrate how the results can be used to gain insights into the evolution of antibiotic resistance and other traits.We envisage SNPPar will help facilitate the undertaking of long-term, real-time surveillance of bacterial pathogens, and their adaptive evolutionary response to interventions and control measures such as new drugs or vaccines.Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article, through supplementary data files or other online sources as indicated in the article.New content generated for this paper is:SNPPar code is available fromhttps://github.com/d-j-e/SNPPar. The version described here is v1.0.A GitHub repository containing the full protocol, ‘in-house’ code and data used to carry out the validation and performance testing is available athttps://github.com/d-j-e/SNPPar_test. This repository includes all the simulated and real data sets used here.Data statementThe authors confirm all supporting data, code and protocols have been provided within the article, through supplementary data files or other online sources as indicated in the article.</jats:sec

[CII] 158 micron Luminosities and Star Formation Rate in Dusty Starbursts and AGN

Results are presented for [CII] 158 micron line fluxes observed with the Herschel PACS instrument in 112 sources with both starburst and AGN classifications, of which 102 sources have confident detections. Results are compared with mid-infrared spectra from the Spitzer Infrared Spectrometer and with L(IR) from IRAS fluxes; AGN/starburst classifications are determined from equivalent width of the 6.2 micron PAH feature. It is found that the [CII] line flux correlates closely with the flux of the 11.3 micron PAH feature independent of AGN/starburst classification, log [f([CII] 158 micron)/f(11.3 micron PAH)] = -0.22 +- 0.25. It is concluded that [CII] line flux measures the photodissociation region associated with starbursts in the same fashion as the PAH feature. A calibration of star formation rate for the starburst component in any source having [CII] is derived comparing [CII] luminosity L([CII]) to L(IR) with the result that log SFR = log L([CII)]) - 7.08 +- 0.3, for SFR in solar masses per year and L([CII]) in solar luminosities. The decreasing ratio of L([CII]) to L(IR) in more luminous sources (the "[CII] deficit") is shown to be a consequence of the dominant contribution to L(IR) arising from a luminous AGN component because the sources with largest L(IR) and smallest L([CII])/L(IR) are AGN.Comment: Accepted for publication in The Astrophysical Journa

Mid-Infrared Spectroscopy of Two Lensed Star-forming Galaxies

We present low-resolution, rest-frame ~ 5 - 12 micron Spitzer/IRS spectra of two lensed z ~ 2 UV-bright star-forming galaxies, SDSS J120602.09+514229.5 and SDSS J090122.37+181432.3. Using the magnification boost from lensing, we are able to study the physical properties of these objects in greater detail than is possible for unlensed systems. In both targets, we detect strong PAH emission at 6.2, 7.7, and 11.3 microns, indicating the presence of vigorous star formation. For J1206, we find a steeply rising continuum and significant [S IV] emission, suggesting that a moderately hard radiation field is powering continuum emission from small dust grains. The strength of the [S IV] emission also implies a sub-solar metallicity of ~ 0.5 Z_{Sun}, confirming published rest-frame optical measurements. In J0901, the PAH lines have large rest-frame equivalent widths (> 1 micron) and the continuum rises slowly with wavelength, suggesting that any AGN contribution to L_{IR} is insignificant, in contrast to the implications of optical emission-line diagnostics. Using [O III] line flux as a proxy for AGN strength, we estimate that the AGN in J0901 provides only a small fraction of its mid-infrared continuum flux. By combining the detection of [Ar II] with an upper limit on [Ar III] emission, we infer a metallicity of > 1.3 Z_{Sun}. This work highlights the importance of combining rest-frame optical and mid-IR spectroscopy in order to understand the detailed properties of star-forming galaxies at high redshift.Comment: 20 pages, 3 figures, 2 tables. ApJ accepte

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/

Beers and blurred boundaries: The spatial and gendered organisation of pre-match venues for English football fans

Academic research into sports fans has grown in recent years with studies examining a variety of aspects associated with fandom. However, recent changes in the professionalisation and commercialisation of sport have resulted in the creation of new spaces for fan experiences. In this article, we examine one of these created spaces, the fan zone. Through a case study on matchgoing fans from Everton Football Club we explore how this new space sits alongside traditional pre-match gathering places such as the ?pub? and examine the gendered organisation of these spaces. Drawing on Bale?s concept of boundaries within sports fan communities we show that traditional venues for pre-match activities enhance, maintain and legitimise masculine boundaries within sports fandom. We argue that fan zones provide an alternative match day atmosphere and experience that is centred on a family-friendly or at least family-inclusive culture

Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression.

BACKGROUND DNA originating from degenerate tumour cells can be detected in the circulation in many tumour types, where it can be used as a marker of disease burden as well as to monitor treatment response. Although circulating tumour DNA (ctDNA) measurement has prognostic/predictive value in metastatic prostate cancer, its utility in localised disease is unknown. METHODS We performed whole-genome sequencing of tumour-normal pairs in eight patients with clinically localised disease undergoing prostatectomy, identifying high confidence genomic aberrations. A bespoke DNA capture and amplification panel against the highest prevalence, highest confidence aberrations for each individual was designed and used to interrogate ctDNA isolated from plasma prospectively obtained pre- and post- (24 h and 6 weeks) surgery. In a separate cohort (n = 189), we identified the presence of ctDNA TP53 mutations in preoperative plasma in a retrospective cohort and determined its association with biochemical- and metastasis-free survival. RESULTS Tumour variants in ctDNA were positively identified pre-treatment in two of eight patients, which in both cases remained detectable postoperatively. Patients with tumour variants in ctDNA had extremely rapid disease recurrence and progression compared to those where variants could not be detected. In terms of aberrations targeted, single nucleotide and structural variants outperformed indels and copy number aberrations. Detection of ctDNA TP53 mutations was associated with a significantly shorter metastasis-free survival (6.2 vs. 9.5 years (HR 2.4; 95% CIs 1.2-4.8, p = 0.014). CONCLUSIONS CtDNA is uncommonly detected in localised prostate cancer, but its presence portends more rapidly progressive disease

Particles and fields in fluid turbulence

The understanding of fluid turbulence has considerably progressed in recent years. The application of the methods of statistical mechanics to the description of the motion of fluid particles, i.e. to the Lagrangian dynamics, has led to a new quantitative theory of intermittency in turbulent transport. The first analytical description of anomalous scaling laws in turbulence has been obtained. The underlying physical mechanism reveals the role of statistical integrals of motion in non-equilibrium systems. For turbulent transport, the statistical conservation laws are hidden in the evolution of groups of fluid particles and arise from the competition between the expansion of a group and the change of its geometry. By breaking the scale-invariance symmetry, the statistically conserved quantities lead to the observed anomalous scaling of transported fields. Lagrangian methods also shed new light on some practical issues, such as mixing and turbulent magnetic dynamo.Comment: 165 pages, review article for Rev. Mod. Phy

Statistical Properties of Turbulence: An Overview

We present an introductory overview of several challenging problems in the statistical characterisation of turbulence. We provide examples from fluid turbulence in three and two dimensions, from the turbulent advection of passive scalars, turbulence in the one-dimensional Burgers equation, and fluid turbulence in the presence of polymer additives.Comment: 34 pages, 31 figure

Herschel-ATLAS: Multi-wavelength SEDs and physical properties of 250 micron-selected galaxies at z < 0.5

We present a pan-chromatic analysis of an unprecedented sample of 1402 250 micron-selected galaxies at z < 0.5 (mean z = 0.24) from the Herschel-ATLAS survey. We complement our Herschel 100-500 micron data with UV-K-band photometry from the Galaxy And Mass Assembly (GAMA) survey and apply the MAGPHYS energy-balance technique to produce pan-chromatic SEDs for a representative sample of 250 micron selected galaxies spanning the most recent 5 Gyr of cosmic history. We derive estimates of physical parameters, including star formation rates, stellar masses, dust masses and infrared luminosities. The typical H-ATLAS galaxy at z < 0.5 has a far-infrared luminosity in the range 10^10 - 10^12 Lsolar (SFR: 1-50 Msolar/yr) thus is broadly representative of normal star forming galaxies over this redshift range. We show that 250 micron-selected galaxies contain a larger mass of dust at a given infra-red luminosity or star formation rate than previous samples selected at 60 micron from IRAS. We derive typical SEDs for H-ATLAS galaxies, and show that the emergent SED shape is most sensitive to specific star formation rate. The optical-UV SEDs also become more reddened due to dust at higher redshifts. Our template SEDs are significantly cooler than existing infra-red templates. They may therefore be most appropriate for inferring total IR luminosities from moderate redshift submillimetre selected samples and for inclusion in models of the lower redshift submillimetre galaxy populations.Comment: 26 pages, 24 figures, Accepted by MNRA