Modular Autoencoders for Ensemble Feature Extraction

We introduce the concept of a Modular Autoencoder (MAE), capable of learning a set of diverse but complementary representations from unlabelled data, that can later be used for supervised tasks. The learning of the representations is controlled by a trade off parameter, and we show on six benchmark datasets the optimum lies between two extremes: a set of smaller, independent autoencoders each with low capacity, versus a single monolithic encoding, outperforming an appropriate baseline. In the present paper we explore the special case of linear MAE, and derive an SVD-based algorithm which converges several orders of magnitude faster than gradient descent.Comment: 18 pages, 8 figures, to appear in a special issue of The Journal Of Machine Learning Research (vol.44, Dec 2015

Enhancement of primary production in the North Atlantic outside of the spring bloom, identified by remote sensing of ocean colour and temperature

Peer reviewedPublisher PD

Scalable quantum computation in systems with Bose-Hubbard dynamics

Several proposals for quantum computation utilize a lattice type architecture with qubits trapped by a periodic potential. For systems undergoing many body interactions described by the Bose-Hubbard Hamiltonian, the ground state of the system carries number fluctuations that scale with the number of qubits. This process degrades the initialization of the quantum computer register and can introduce errors during error correction. In an earlier manuscript we proposed a solution to this problem tailored to the loading of cold atoms into an optical lattice via the Mott Insulator phase transition. It was shown that by adding an inhomogeneity to the lattice and performing a continuous measurement, the unit filled state suitable for a quantum computer register can be maintained. Here, we give a more rigorous derivation of the register fidelity in homogeneous and inhomogeneous lattices and provide evidence that the protocol is effective in the finite temperature regime.Comment: 12 pages, 3 figures. Expanded version of manuscript submitted to the Journal of Modern Optics. v2 corrects typesetting error in Fig.

Human cytomegalovirus: taking the strain

In celebrating the 60th anniversary of the first isolation of human cytomegalovirus (HCMV), we reflect on the merits and limitations of the viral strains currently being used to develop urgently needed treatments. HCMV research has been dependent for decades on the high-passage strains AD169 and Towne, heavily exploiting their capacity to replicate efficiently in fibroblasts. However, the genetic integrity of these strains is so severely compromised that great caution needs to be exercised when considering their past and future use. It is now evident that wild-type HCMV strains are not readily propagated in vitro. HCMV mutants are rapidly selected during isolation in fibroblasts, reproducibly affecting gene RL13, the UL128 locus (which includes genes UL128, UL130 and UL131A) and often the UL/b′ region. As a result, the virus becomes less cell associated, altered in tropism and less pathogenic. This problem is not restricted to high-passage strains, as even low-passage strains can harbour biologically significant mutations. Cloning and manipulation of the HCMV genome as a bacterial artificial chromosome (BAC) offers a means of working with stable, genetically defined strains. To this end, the low-passage strain Merlin genome was cloned as a BAC and sequentially repaired to match the viral sequence in the original clinical sample from which Merlin was derived. Restoration of UL128L to wild type was detrimental to growth in fibroblasts, whereas restoration of RL13 impaired growth in all cell types tested. Stable propagation of phenotypically wild-type virus could be achieved only by placing both regions under conditional expression. In addition to the development of these tools, the Merlin transcriptome and proteome have been characterized in unparalleled detail. Although Merlin may be representative of the clinical agent, high-throughput whole-genome deep sequencing studies have highlighted the remarkable high level of interstrain variation present in circulating virus. There is a need to develop systems capable of addressing the significance of this diversity, free from the confounding effects of genetic changes associated with in vitro adaptation. The generation of a set of BAC clones, each containing the genome of a different HCMV strain repaired to match the sequence in the clinical sample, would provide a pathway to address the biological and clinical effects of natural variation in wild-type HCMV

Scalable register initialization for quantum computing in an optical lattice

The Mott insulator state created by loading an atomic Bose-Einstein condensate (BEC) into an optical lattice may be used as a means to prepare a register of atomic qubits in a quantum computer. Such architecture requires a lattice commensurately filled with atoms, which corresponds to the insulator state only in the limit of zero inter-well tunneling. We show that a lattice with spatial inhomogeneity created by a quadratic magnetic trapping potential can be used to isolate a subspace in the center which is impervious to hole-hoping. Components of the wavefunction with more than one atom in any well can be projected out by selective measurement on a molecular photo-associative transition. Maintaining the molecular coupling induces a quantum Zeno effect that can sustain a commensurately filled register for the duration of a quantum computation.Comment: 5 pages, 2 figure

Anisotropic J/ΨJ/\Psi suppression in nuclear collisions

The nuclear overlap zone in non-central relativistic heavy ion collisions is azimuthally very asymmetric. By varying the angle between the axes of deformation and the transverse direction of the pair momenta, the suppression of $J/\Psi$ and $\Psi'$ will oscillate in a characteristic way. Whereas the average suppression is mostly sensitive to the early and high density stages of the collision, the amplitude is more sensitive to the late stages. This effect provides additional information on the $J/\Psi$ suppression mechanisms such as direct absorption on participating nucleons, comover absorption or formation of a quark-gluon plasma. The behavior of the average $J/\Psi$ suppression and its amplitude with centrality of the collisions is discussed for SPS, RHIC and LHC energies with and without a phase transition.Comment: Revised and extended version, new figure

Inkjet printing of oral dosage forms to solubilize BCS Class II drugs

Oral drug delivery remains the preferred method of administration but BCS Class II drugs are not ideally suited to this due to their inherent poor solubility. Although a number of methods to increase solubility already exist, there is a need for less damaging methods of production which are more flexible to the needs of the patient. The innovative formulation method of inkjet printing has been suggested for this purpose as it has the capacity to produce highly precise dosing in a continuous manner. The Optomec Aerosol Jet 200 Printer utilised in the current study has never been used in pharmaceutical research before and it is highly interesting as it functions in a manner akin to a miniaturised spray dryer. Due to the low dose content of a single layer, formulations can be easily tailored to the patient’s individual requirements by changing the size and speed of deposition, utilising different nozzle sizes and layering to increase the overall dose. Raman spectroscopy, scanning electron microscopy and powder x-ray diffraction suggest that printing the drug alone results in a crystalline product. However, in the presence of a polymer it seems to form a less crystalline product suggesting the polymer is promoting solid dispersion formation in a similar manner to a spray dryer. Completely amorphous formulations are achieved on application of a premixed "ink" with a polymer content of 75% or more, allowing up to 25% drug loading. Drug release increases 10-fold on printing relative to a comparable powder blend and thus inkjet printing can be considered to be a viable method of improving the overall performance of the drug. The next steps will be to utilize this established methodology to produce innovative controlled release on a small scale

Inkjet printing oral dosage forms

The current study aims to establish an innovative method of effectively solubilising Biopharmaceutical Classification System Class II drugs using inkjet printing. Dosage forms have been produced using an Optomec AJ200 3D Inkjet printer. Printing with an appropriate polymer seems to result in an amorphous product, which will hopefully have a greater overall solubility