Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

DECC/BGS assessment of resource potential of the Bowland Shale, UK

This paper reviews the results of the DECC-commissioned 2012-13 BGS study to estimate the shale gas resource assessment of the Carboniferous Bowland Shale in central Great Britain. Over 15,000 miles of seismic data were interpreted and integrated with well and outcrop control, BGS mapping, 3D depth modelling, geochemical analysis, and 2D thermal maturity basin modelling. The Bowland Shale, and its laterally equivalent basinal shale formations are known to be important source rocks. The study recognised two depositional units; an organic-rich upper part that is a widespread marine shale unit drowning most platform highs and a lower unit comprised of very thick rift-basin fill shales with mass-flow carbonates and rare mass-flow sandstones, passing laterally to platform carbonates on the paleo-highs. An interpreted top gas window thermal maturity surface was integrated with the depth structure mapping to identify the volume of Bowland shale in the gas window which was used as one of the input parameters for a Monte Carlo simulation of the in-place gas resources. The study estimates a large volume of gas in the shales beneath the UK, but concludes that not enough is known yet to estimate a recovery factor, nor to estimate potential reserves

Order Parameters of the Dilute A Models

The free energy and local height probabilities of the dilute A models with broken \Integer_2 symmetry are calculated analytically using inversion and corner transfer matrix methods. These models possess four critical branches. The first two branches provide new realisations of the unitary minimal series and the other two branches give a direct product of this series with an Ising model. We identify the integrable perturbations which move the dilute A models away from the critical limit. Generalised order parameters are defined and their critical exponents extracted. The associated conformal weights are found to occur on the diagonal of the relevant Kac table. In an appropriate regime the dilute A$_3$ model lies in the universality class of the Ising model in a magnetic field. In this case we obtain the magnetic exponent $\delta=15$ directly, without the use of scaling relations.Comment: 53 pages, LaTex, ITFA 93-1

On the stability of standing matter waves in a trap

We discuss excited Bose-condensed states and find the criterion of dynamical stability of a kink-wise state, i.e., a standing matter wave with one nodal plane perpendicular to the axis of a cylindrical trap. The dynamical stability requires a strong radial confinement corresponding to the radial frequency larger than the mean-field interparticle interaction. We address the question of thermodynamic instability related to the presence of excitations with negative energy.Comment: 4 pages, 3 figure

The Bogoliubov Theory of a BEC in Particle Representation

In the number-conserving Bogoliubov theory of BEC the Bogoliubov transformation between quasiparticles and particles is nonlinear. We invert this nonlinear transformation and give general expression for eigenstates of the Bogoliubov Hamiltonian in particle representation. The particle representation unveils structure of a condensate multiparticle wavefunction. We give several examples to illustrate the general formalism.Comment: 10 pages, 9 figures, version accepted for publication in Phys. Rev.

Information transfer through disordered media by diffuse waves

We consider the information content h of a scalar multiple-scattered, diffuse wave field $\psi(\vec{r})$ and the information capacity C of a communication channel that employs diffuse waves to transfer the information through a disordered medium. Both h and C are shown to be directly related to the mesoscopic correlations between the values of $\psi(\vec{r})$ at different positions $\vec{r}$ in space, arising due to the coherent nature of the wave. For the particular case of a communication channel between two identical linear arrays of $n \gg 1$ equally-spaced transmitters/receivers (receiver spacing a), we show that the average capacity $\propto n$ and obtain explicit analytic expressions for $/n$ in the limit of $n \to \infty$ and $k \ell \to \infty$, where $k= 2\pi/ \lambda$, $\lambda$ is the wavelength, and $\ell$ is the mean free path. Modification of the above results in the case of finite but large n and $k \ell$ is discussed as well.Comment: REVTeX 4, 12 pages, 7 figure

Anomalous rotational properties of Bose-Einstein condensates in asymmetric traps

We study the rotational properties of a Bose-Einstein condensate confined in a rotating harmonic trap for different trap anisotropies. Using simple arguments, we derive expressions for the velocity field of the quantum fluid for condensates with or without vortices. While the condensed gas describes open spiraling trajectories, on the frame of reference of the rotating trap the motion of the fluid is against the trap rotation. We also find explicit formulae for the angular momentum and a linear and Thomas-Fermi solutions for the state without vortices. In these two limits we also find an analytic relation between the shape of the cloud and the rotation speed. The predictions are supported by numerical simulations of the mean field Gross-Pitaevskii model.Comment: 4 RevTeX pages, 2 EPS figures; typos fixed, reference adde

[Accepted Manuscript] A call to strengthen the global strategy against schistosomiasis and soil-transmitted helminthiasis: the time is now.

In 2001, the World Health Assembly (WHA) passed the landmark WHA 54.19 resolution for global scale-up of mass administration of anthelmintic drugs for morbidity control of schistosomiasis and soil-transmitted helminthiasis, which affect more than 1·5 billion of the world's poorest people. Since then, more than a decade of research and experience has yielded crucial knowledge on the control and elimination of these helminthiases. However, the global strategy has remained largely unchanged since the original 2001 WHA resolution and associated WHO guidelines on preventive chemotherapy. In this Personal View, we highlight recent advances that, taken together, support a call to revise the global strategy and guidelines for preventive chemotherapy and complementary interventions against schistosomiasis and soil-transmitted helminthiasis. These advances include the development of guidance that is specific to goals of morbidity control and elimination of transmission. We quantify the result of forgoing this opportunity by computing the yearly disease burden, mortality, and lost economic productivity associated with maintaining the status quo. Without change, we estimate that the population of sub-Saharan Africa will probably lose 2·3 million disability-adjusted life-years and US$3·5 billion of economic productivity every year, which is comparable to recent acute epidemics, including the 2014 Ebola and 2015 Zika epidemics. We propose that the time is now to strengthen the global strategy to address the substantial disease burden of schistosomiasis and soil-transmitted helminthiasis

New strings for old Veneziano amplitudes II. Group-theoretic treatment

In this part of our four parts work (e.g see Part I, hep-th/0410242) we use the theory of polynomial invariants of finite pseudo-reflection groups in order to reconstruct both the Veneziano and Veneziano-like (tachyon-free) amplitudes and the generating function reproducing these amplitudes. We demonstrate that such generating function can be recovered with help of the finite dimensional exactly solvable N=2 supersymmetric quantum mechanical model known earlier from works by Witten, Stone and others. Using the Lefschetz isomorphisms theorem we replace traditional supersymmetric calculations by the group-theoretic thus solving the Veneziano model exactly using standard methods of representation theory. Mathematical correctness of our arguments relies on important theorems by Shepard and Todd, Serre and Solomon proven respectively in early fifties and sixties and documented in the monograph by Bourbaki. Based on these theorems we explain why the developed formalism leaves all known results of conformal field theories unchanged. We also explain why these theorems impose stringent requirements connecting analytical properties of scattering amplitudes with symmetries of space-time in which such amplitudes act.Comment: 57 pages J.Geom.Phys.(in press, available on line

Solutions of Gross-Pitaevskii equations beyond the hydrodynamic approximation: Application to the vortex problem

We develop the multiscale technique to describe excitations of a Bose-Einstein condensate (BEC) whose characteristic scales are comparable with the healing length, thus going beyond the conventional hydrodynamical approximation. As an application of the theory we derive approximate explicit vortex and other solutions. The dynamical stability of the vortex is discussed on the basis of the mathematical framework developed here, the result being that its stability is granted at least up to times of the order of seconds, which is the condensate lifetime. Our analytical results are confirmed by the numerical simulations.Comment: To appear in Phys. Rev.