Discovering transcriptional modules by Bayesian data integration

Motivation: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets. Results: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs

Exploiting Temporal Complex Network Metrics in Mobile Malware Containment

Malicious mobile phone worms spread between devices via short-range Bluetooth contacts, similar to the propagation of human and other biological viruses. Recent work has employed models from epidemiology and complex networks to analyse the spread of malware and the effect of patching specific nodes. These approaches have adopted a static view of the mobile networks, i.e., by aggregating all the edges that appear over time, which leads to an approximate representation of the real interactions: instead, these networks are inherently dynamic and the edge appearance and disappearance is highly influenced by the ordering of the human contacts, something which is not captured at all by existing complex network measures. In this paper we first study how the blocking of malware propagation through immunisation of key nodes (even if carefully chosen through static or temporal betweenness centrality metrics) is ineffective: this is due to the richness of alternative paths in these networks. Then we introduce a time-aware containment strategy that spreads a patch message starting from nodes with high temporal closeness centrality and show its effectiveness using three real-world datasets. Temporal closeness allows the identification of nodes able to reach most nodes quickly: we show that this scheme can reduce the cellular network resource consumption and associated costs, achieving, at the same time, a complete containment of the malware in a limited amount of time.Comment: 9 Pages, 13 Figures, In Proceedings of IEEE 12th International Symposium on a World of Wireless, Mobile and Multimedia Networks (WOWMOM '11

Efficient photon number detection with silicon avalanche photodiodes

We demonstrate an efficient photon number detector for visible wavelengths using a silicon avalanche photodiode. Under subnanosecond gating, the device is able to resolve up to four photons in an incident optical pulse. The detection efficiency at 600 nm is measured to be 73.8%, corresponding to an avalanche probability of 91.1% of the absorbed photons, with a dark count probability below 1.1x10^{-6} per gate. With this performance and operation close to room temperature, fast-gated silicon avalanche photodiodes are ideal for optical quantum information processing that requires single-shot photon number detection

Visual distortion of body size modulates pain perception

Pain is a complex subjective experience, that can be shaped by several cognitive, psychological and even contextual variables. For example, simply viewing the body reduces the reported intensity of acute physical pain. We investigated whether this visually induced analgesia can be modulated by the visually depicted size of the stimulated body part. We measured contact heat-pain thresholds, while participants viewed either their own hand or a neutral object, at real size, enlarged, or reduced. Vision of the body was analgesic, increasing heat-pain thresholds by ~ 4°C. Importantly, enlargement of the viewed hand enhanced this analgesia, while looking at a reduced hand decreased it. These results demonstrate that visual distortions of body size modulate sensory components of pain, and reveal a clear functional relation between the perception of pain and the representation of the body

Plans for laser spectroscopy of trapped cold hydrogen-like HCI

Laser spectroscopy studies are being prepared to measure the 1s ground state hyperfine splitting in trapped cold highly charged ions. The purpose of such experiments is to test quantum electrodynamics in the strong electric field regime. These experiments form part of the HITRAP project at GSI. A brief review of the planned experiments is presented.Comment: 4 pages, 4 figures, accepted for publication (NIMB

Potential of a cyclone prototype spacer to improve in vitro dry powder delivery

Copyright The Author(s) 2013. This article is published with open access at Springerlink.com. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are creditedPurpose: Low inspiratory force in patients with lung disease is associated with poor deagglomeration and high throat deposition when using dry powder inhalers (DPIs). The potential of two reverse flow cyclone prototypes as spacers for commercial carrierbased DPIs was investigated. Methods: Cyclohaler®, Accuhaler® and Easyhaler® were tested with and without the spacers between 30-60 Lmin-1. Deposition of particles in the next generation impactor and within the devices was determined by high performance liquid chromatography. Results: Reduced induction port deposition of the emitted particles from the cyclones was observed due to the high retention of the drug within the spacers (e.g. salbutamol sulphate (SS): 67.89 ± 6.51 % at 30 Lmin-1 in Cheng 1). Fine particle fractions of aerosol as emitted from the cyclones were substantially higher than the DPIs alone. Moreover, the aerodynamic diameters of particles emitted from the cyclones were halved compared to the DPIs alone (e.g. SS from the Cyclohaler® at 4 kPa: 1.08 ± 0.05 μm vs. 3.00 ± 0.12 μm, with and without Cheng 2, respectively) and unaltered with increased flow rates. Conclusion: This work has shown the potential of employing a cyclone spacer for commercial carrier-based DPIs to improve inhaled drug delivery.Peer reviewe

Developing a National Design Scoreboard

Recognising the growing importance of design, this paper reports on the development of an approach to measuring design at a national level. A series of measures is proposed, that are based around a simplified model of design as a system at a national level. This model was developed though insights from literature and a workshop with government, industry and design sector representatives. Detailed data on design in the UK is presented to highlight the difficulties in collecting reliable and robust data. Evidence is compared with four countries (Spain, Canada, Korea and Sweden). This comparison highlights the inherent difficulties in comparing performance and a revised set of measures is proposed. Finally, an approach to capturing design spend at a firm level is proposed, based on insights from literature and case studies. Keywords: National Design System, Design Performance</p

Characterisation of friction and lubrication regimes in premium tubular connections

A friction test rig has been developed to carry out repeated sliding friction tests for premium tubular connections. The test rig enables accurate measurement of friction in various contact regimes which are relevant to the threaded connections between tubular components. Higher load tests can simulate the contact in metal-to-metal seals under very high contact pressures by using perpendicular pin-on-pin tests. The contact in the thread loading flank under intermediate pressures can be simulated by using larger radius coupon-on-coupon tests. The measured coefficient of friction is well correlated with a lubrication parameter combining lubricant film thickness and initial surface roughness. © 2012 Elsevier Ltd. All rights reserved

Optimal edge termination for high oxide reliability aiming 10kV SiC n-IGBTs

The edge termination design strongly affects the ability of a power device to support the desired voltage and its reliable operation. In this paper we present three appropriate termination designs for 10kV n-IGBTs which achieve the desired blocking requirement without the need for deep and expensive implantations. Thus, they improve the ability to fabricate, minimise the cost and reduce the lattice damage due to the high implantation energy. The edge terminations presented are optimised both for achieving the widest immunity to dopant activation and to minimise the electric field at the oxide. Thus, they ensure the long-term reliability of the device. This work has shown that the optimum design for blocking voltage and widest dose window does not necessarily give the best design for reliability. Further, it has been shown that Hybrid Junction Termination Extension structure with Space Modulated Floating Field Rings can give the best result of very high termination efficiency, as high as 99%, the widest doping variation immunity and the lowest electric field in the oxide

Low-Density Parity-Check Codes for Nonergodic Block-Fading Channels

We solve the problem of designing powerful low-density parity-check (LDPC) codes with iterative decoding for the block-fading channel. We first study the case of maximum-likelihood decoding, and show that the design criterion is rather straightforward. Unfortunately, optimal constructions for maximum-likelihood decoding do not perform well under iterative decoding. To overcome this limitation, we then introduce a new family of full-diversity LDPC codes that exhibit near-outage-limit performance under iterative decoding for all block-lengths. This family competes with multiplexed parallel turbo codes suitable for nonergodic channels and recently reported in the literature.Comment: Submitted to the IEEE Transactions on Information Theor