Ultraviolet asymptotics of scalar and pseudoscalar correlators in hot Yang-Mills theory

Inspired by recent lattice measurements, we determine the short-distance (a > omega >> pi T) asymptotics of scalar (trace anomaly) and pseudoscalar (topological charge density) correlators at 2-loop order in hot Yang-Mills theory. The results are expressed in the form of an Operator Product Expansion. We confirm and refine the determination of a number of Wilson coefficients; however some discrepancies with recent literature are detected as well, and employing the correct values might help, on the qualitative level, to understand some of the features observed in the lattice measurements. On the other hand, the Wilson coefficients show slow convergence and it appears uncertain whether this approach can lead to quantitative comparisons with lattice data. Nevertheless, as we outline, our general results might serve as theoretical starting points for a number of perhaps phenomenologically more successful lines of investigation.Comment: 27 pages. v2: minor improvements, published versio

The role of galaxies and AGN in reionising the IGM -- III : IGM-galaxy cross-correlations at z~6 from 8 quasar fields with DEIMOS and MUSE

We present improved results of the measurement of the correlation between galaxies and the intergalactic medium transmission at the end of reionization. We have gathered a sample of 13 spectroscopically confirmed Lyman-break galaxies (LBGs) and 21 Lyman-α emitters (LAEs) at angular separations 20 arcsec ≲ θ ≲ 10 arcmin (∼0.1–4 pMpc at z ∼ 6) from the sightlines to eight background z ≳ 6 quasars. We report for the first time the detection of an excess of Lyman-α transmission spikes at ∼10–60 cMpc from LAEs (3.2σ) and LBGs (1.9σ). We interpret the data with an improved model of the galaxy–Lyman-α transmission and two-point cross-correlations, which includes the enhanced photoionization due to clustered faint sources, enhanced gas densities around the central bright objects and spatial variations of the mean free path. The observed LAE(LBG)–Lyman-α transmission spike two-point cross-correlation function (2PCCF) constrains the luminosity-averaged escape fraction of all galaxies contributing to reionization to ⟨fesc⟩MUV−20(2σ)⁠) is necessary to reproduce the observed 2PCCF and that reionization might be driven by different sub-populations around LBGs and LAEs at z ∼ 6

Hydrological (in)stability in Southern Siberia during the Younger Dryas and early Holocene

Southern Siberia is currently undergoing rapid warming, inducing changes in vegetation, loss of permafrost, and impacts on the hydrodynamics of lakes and rivers. Lake sediments are key archives of environmental change and contain a record of ecosystem variability, as well as providing proxy indicators of wider environmental and climatic change. Investigating how hydrological systems have responded to past shifts in climate can provide essential context for better understanding future ecosystem changes in Siberia. Oxygen isotope ratios within lacustrine records provide fundamental information on past variability in hydrological systems. Here we present a new oxygen isotope record from diatom silica (ẟ18Odiatom) at Lake Baunt (55°11′15″N, 113°01,45″E), in the southern part of eastern Siberia, and consider how the site has responded to climate changes between the Younger Dryas and Early to Mid Holocene (ca. 12.4 to 6.2 ka cal BP). Excursions in ẟ18Odiatom are influenced by air temperature and the seasonality, quantity, and source of atmospheric precipitation. These variables are a function of the strength of the Siberian High, which controls temperature, the proportion and quantity of winter versus summer precipitation, and the relative dominance of Atlantic versus Pacific air masses. A regional comparison with other Siberian ẟ18Odiatom records, from lakes Baikal and Kotokel, suggests that ẟ18Odiatom variations in southern Siberia reflect increased continentality during the Younger Dryas, delayed Early Holocene warming in the region, and substantial climate instability between ~10.5 to ~8.2 ka cal BP. Unstable conditions during the Early Holocene thermal optimum most likely reflect localised changes from glacial melting. Taking the profiles from three very different lakes together, highlight the influence of site specific factors on the individual records, and how one site is not indicative of the region as a whole. Overall, the study documents how sensitive this important region is to both internal and external forcing

Automatically extracting functionally equivalent proteins from SwissProt

In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot

Probing strongly coupled anisotropic plasma

We calculate the static potential, the drag force and the jet quenching parameter in strongly coupled anisotropic N=4 super Yang-Mills plasma. We find that the jet quenching is in general enhanced in presence of anisotropy compared to the isotropic case and that its value depends strongly on the direction of the moving quark and the direction along which the momentum broadening occurs. The jet quenching is strongly enhanced for a quark moving along the anisotropic direction and momentum broadening happens along the transverse one. The parameter gets lower for a quark moving along the transverse direction and the momentum broadening considered along the anisotropic one. Finally, a weaker enhancement is observed when the quark moves in the transverse plane and the broadening occurs on the same plane. The drag force for quark motion parallel to the anisotropy is always enhanced. For motion in the transverse space the drag force is enhanced compared to the isotropic case only for quarks having velocity above a critical value. Below this critical value the force is decreased. Moreover, the drag force along the anisotropic direction is always stronger than the force in the transverse space. The diffusion time follows exactly the inverse relations of the drag forces. The static potential is decreased and stronger decrease observed for quark-antiquark pair aligned along the anisotropic direction than the transverse one. We finally comment on our results and elaborate on their similarities and differences with the weakly coupled plasmas.Comment: 1+44 pages, 18 Figures; Added results on static force; Added references; version published in JHE

Thermal photons in QGP and non-ideal effects

We investigate the thermal photon production-rates using one dimensional boost-invariant second order relativistic hydrodynamics to find proper time evolution of the energy density and the temperature. The effect of bulk-viscosity and non-ideal equation of state are taken into account in a manner consistent with recent lattice QCD estimates. It is shown that the \textit{non-ideal} gas equation of state i.e $\epsilon-3\,P\,\neq 0$ behaviour of the expanding plasma, which is important near the phase-transition point, can significantly slow down the hydrodynamic expansion and thereby increase the photon production-rates. Inclusion of the bulk viscosity may also have similar effect on the hydrodynamic evolution. However the effect of bulk viscosity is shown to be significantly lower than the \textit{non-ideal} gas equation of state. We also analyze the interesting phenomenon of bulk viscosity induced cavitation making the hydrodynamical description invalid. We include the viscous corrections to the distribution functions while calculating the photon spectra. It is shown that ignoring the cavitation phenomenon can lead to erroneous estimation of the photon flux.Comment: 11 pages, 13 figures; accepted for publication in JHE

Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism.

Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology

Disease progression in Plasmodium knowlesi malaria is linked to variation in invasion gene family members.

Emerging pathogens undermine initiatives to control the global health impact of infectious diseases. Zoonotic malaria is no exception. Plasmodium knowlesi, a malaria parasite of Southeast Asian macaques, has entered the human population. P. knowlesi, like Plasmodium falciparum, can reach high parasitaemia in human infections, and the World Health Organization guidelines for severe malaria list hyperparasitaemia among the measures of severe malaria in both infections. Not all patients with P. knowlesi infections develop hyperparasitaemia, and it is important to determine why. Between isolate variability in erythrocyte invasion, efficiency seems key. Here we investigate the idea that particular alleles of two P. knowlesi erythrocyte invasion genes, P. knowlesi normocyte binding protein Pknbpxa and Pknbpxb, influence parasitaemia and human disease progression. Pknbpxa and Pknbpxb reference DNA sequences were generated from five geographically and temporally distinct P. knowlesi patient isolates. Polymorphic regions of each gene (approximately 800 bp) were identified by haplotyping 147 patient isolates at each locus. Parasitaemia in the study cohort was associated with markers of disease severity including liver and renal dysfunction, haemoglobin, platelets and lactate, (r = ≥ 0.34, p =  <0.0001 for all). Seventy-five and 51 Pknbpxa and Pknbpxb haplotypes were resolved in 138 (94%) and 134 (92%) patient isolates respectively. The haplotypes formed twelve Pknbpxa and two Pknbpxb allelic groups. Patients infected with parasites with particular Pknbpxa and Pknbpxb alleles within the groups had significantly higher parasitaemia and other markers of disease severity. Our study strongly suggests that P. knowlesi invasion gene variants contribute to parasite virulence. We focused on two invasion genes, and we anticipate that additional virulent loci will be identified in pathogen genome-wide studies. The multiple sustained entries of this diverse pathogen into the human population must give cause for concern to malaria elimination strategists in the Southeast Asian region

Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes.

The data set supporting the results of this article is available in the Dryad repository, http://dx.doi.org/10.5061/dryad.6f4qs. Moustakas, A. and Evans, M. R. (2015) Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values.Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose

Extracellular ATP is a pro-angiogenic factor for pulmonary artery vasa vasorum endothelial cells

Expansion of the vasa vasorum network has been observed in a variety of systemic and pulmonary vascular diseases. We recently reported that a marked expansion of the vasa vasorum network occurs in the pulmonary artery adventitia of chronically hypoxic calves. Since hypoxia has been shown to stimulate ATP release from both vascular resident as well as circulatory blood cells, these studies were undertaken to determine if extracellular ATP exerts angiogenic effects on isolated vasa vasorum endothelial cells (VVEC) and/or if it augments the effects of other angiogenic factors (VEGF and basic FGF) known to be present in the hypoxic microenvironment. We found that extracellular ATP dramatically increases DNA synthesis, migration, and rearrangement into tube-like networks on Matrigel in VVEC, but not in pulmonary artery (MPAEC) or aortic (AOEC) endothelial cells obtained from the same animals. Extracellular ATP potentiated the effects of both VEGF and bFGF to stimulate DNA synthesis in VVEC but not in MPAEC and AOEC. Analysis of purine and pyrimidine nucleotides revealed that ATP, ADP and MeSADP were the most potent in stimulating mitogenic responses in VVEC, indicating the involvement of the family of P2Y1-like purinergic receptors. Using pharmacological inhibitors, Western blot analysis, and Phosphatidylinositol-3 kinase (PI3K) in vitro kinase assays, we found that PI3K/Akt/mTOR and ERK1/2 play a critical role in mediating the extracellular ATP-induced mitogenic and migratory responses in VVEC. However, PI3K/Akt and mTOR/p70S6K do not significantly contribute to extracellular ATP-induced tube formation on Matrigel. Our studies indicate that VVEC, isolated from the sites of active angiogenesis, exhibit distinct functional responses to ATP, compared to endothelial cells derived from large pulmonary or systemic vessels. Collectively, our data support the idea that extracellular ATP participates in the expansion of the vasa vasorum that can be observed in hypoxic conditions