4,833 research outputs found
Gravitational Instantons, Confocal Quadrics and Separability of the Schr\"odinger and Hamilton-Jacobi equations
A hyperk\"ahler 4-metric with a triholomorphic SU(2) action gives rise to a
family of confocal quadrics in Euclidean 3-space when cast in the canonical
form of a hyperk\"ahler 4-metric metric with a triholomorphic circle action.
Moreover, at least in the case of geodesics orthogonal to the U(1) fibres, both
the covariant Schr\"odinger and the Hamilton-Jacobi equation is separable and
the system integrable.Comment: 10 pages Late
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Evolutionary bi-stability in pathogen transmission mode
Many pathogens transmit to new hosts by both infection (horizontal transmission) and transfer to the
infected host's offspring (vertical transmission). These two transmission modes require speci®c adap-
tations of the pathogen that can be mutually exclusive, resulting in a trade-off between horizontal and
vertical transmission. We show that in mathematical models such trade-offs can lead to the simultaneous
existence of two evolutionary stable states (evolutionary bi-stability) of allocation of resources to the two
modes of transmission. We also show that jumping between evolutionary stable states can be induced by
gradual environmental changes. Using quantitative PCR-based estimates of abundance in seed and vege-
tative parts, we show that the pathogen of wheat, Phaeosphaeria nodorum, has jumped between two
distinct states of transmission mode twice in the past 160 years, which, based on published evidence,
we interpret as adaptation to environmental change. The ®nding of evolutionary bi-stability has impli-
cations for human, animal and other plant diseases. An ill-judged change in a disease control
programme could cause the pathogen to evolve a new, and possibly more damaging, combination of
transmission modes. Similarly, environmental changes can shift the balance between transmission
modes, with adverse effects on human, animal and plant health
Equilibrium solvation in quadrupolar solvents
We present a microscopic theory of equilibrium solvation in solvents with
zero dipole moment and non-zero quadrupole moment (quadrupolar solvents). The
theory is formulated in terms of autocorrelation functions of the quadrupolar
polarization (structure factors). It can be therefore applied to an arbitrary
dense quadrupolar solvent for which the structure factors are defined. We
formulate a simple analytical perturbation treatment for the structure factors.
The solute is described by coordinates, radii, and partial charges of
constituent atoms. The theory is tested on Monte Carlo simulations of solvation
in model quadrupolar solvents. It is also applied to the calculation of the
activation barrier of electron transfer reactions in a cleft-shaped
donor-acceptor complex dissolved in benzene with the structure factors of
quadrupolar polarization obtained from Molecular Dynamics simulations.Comment: Submitted to J. Chem. Phys., 20 pages and 13 figure
The bolometric and UV attenuation in normal spiral galaxies of the Herschel Reference Survey
The dust in nearby galaxies absorbs a fraction of the
UV-optical-near-infrared radiation produced by stars. This energy is
consequently re-emitted in the infrared. We investigate the portion of the
stellar radiation absorbed by spiral galaxies from the HRS by modelling their
UV-to-submillimetre spectral energy distributions. Our models provide an
attenuated and intrinsic SED from which we find that on average 32 % of all
starlight is absorbed by dust. We define the UV heating fraction as the
percentage of dust luminosity that comes from absorbed UV photons and find that
this is 56 %, on average. This percentage varies with morphological type, with
later types having significantly higher UV heating fractions. We find a strong
correlation between the UV heating fraction and specific star formation rate
and provide a power-law fit. Our models allow us to revisit the IRX-AFUV
relations, and derive these quantities directly within a self-consistent
framework. We calibrate this relation for different bins of NUV-r colour and
provide simple relations to relate these parameters. We investigated the
robustness of our method and we conclude that the derived parameters are
reliable within the uncertainties which are inherent to the adopted SED model.
This calls for a deeper investigation on how well extinction and attenuation
can be determined through panchromatic SED modelling.Comment: 14 pages, 7 figures. Accepted for publication in Astronomy &
Astrophysic
Dust emission at 8-mic and 24-mic as Diagnostics of HII Region Radiative Transfer
We use the Spitzer SAGE survey of the Magellanic Clouds to evaluate the
relationship between the 8-mic PAH emission, 24-mic hot dust emission, and HII
region radiative transfer. We confirm that in the higher-metallicity Large
Magellanic Cloud, PAH destruction is sensitive to optically thin conditions in
the nebular Lyman continuum: objects identified as optically thin candidates
based on nebular ionization structure show 6 times lower median 8-mic surface
brightness (0.18 mJy arcsec^-2) than their optically thick counterparts (1.2
mJy arcsec^-2). The 24-mic surface brightness also shows a factor of 3 offset
between the two classes of objects (0.13 vs 0.44 mJy arcsec^-2, respectively),
which is driven by the association between the very small dust grains and
higher density gas found at higher nebular optical depths. In contrast, PAH and
dust formation in the low-metallicity Small Magellanic Cloud is strongly
inhibited such that we find no variation in either 8-mic or 24-mic emission
between our optically thick and thin samples. This is attributable to extremely
low PAH and dust production together with high, corrosive UV photon fluxes in
this low-metallicity environment. The dust mass surface densities and
gas-to-dust ratios determined from dust maps using Herschel HERITAGE survey
data support this interpretation.Comment: Accepted to ApJ, May 15, 2017. 10 pages, 9 figure
OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets
Background: Ovarian cancer has the lowest survival rate of all gynaecologic cancers and is characterised by a lack of early symptoms and frequent late stage diagnosis. There is a paucity of robust molecular markers that are independent of and complementary to clinical parameters such as disease stage and tumour grade.
METHODS: We have developed a user-friendly, web-based system to evaluate the association of genes/miRNAs with outcome in ovarian cancer. The OvMark algorithm combines data from multiple microarray platforms (including probesets targeting miRNAs) and correlates them with clinical parameters (e.g. tumour grade, stage) and outcomes (disease free survival (DFS), overall survival). In total, OvMark combines 14 datasets from 7 different array platforms measuring the expression of ~17,000 genes and 341 miRNAs across 2,129 ovarian cancer samples.
RESULTS: To demonstrate the utility of the system we confirmed the prognostic ability of 14 genes and 2 miRNAs known to play a role in ovarian cancer. Of these genes, CXCL12 was the most significant predictor of DFS (HR = 1.42, p-value = 2.42x10-6). Surprisingly, those genes found to have the greatest correlation with outcome have not been heavily studied in ovarian cancer, or in some cases in any cancer. For instance, the three genes with the greatest association with survival are SNAI3, VWA3A and DNAH12.
CONCLUSIONS/IMPACT:
OvMark is a powerful tool for examining putative gene/miRNA prognostic biomarkers in ovarian cancer (available at http://glados.ucd.ie/OvMark/index.html). The impact of this tool will be in the preliminary assessment of putative biomarkers in ovarian cancer, particularly for research groups with limited bioinformatics facilities
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