Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data

We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

Consensus under general convexity

A method is proposed to characterize contraction of a set through orthogonal projections. For discrete-time multi-agent systems, quantitative estimates of convergence (to a consensus) rate are provided by means of contracting convex sets. Required convexity for the sets that should include the values that the transition maps of agents take is considered in a more general sense than that of Euclidean geometry. © 2007 IEEE.

Effects of the biodiesel fuel physical properties on the swirl stabilised spray combustion characteristics

An increasin g interest in biofuel applications in modern engines requires a better understanding of biodiesel combustion behaviour. Many numerical studies have been carried out on unsteady combustion of biodiesel in situations similar to diesel engines, but very few studies have been done on the steady combustion of biodiesel in situations similar to a gas turbine combustor environment. The study of biodiesel spray combustion in gas turbine applications is of special interest due to the possible use of biodiesel in the power generation and aviation industries. In modelling spray combustion, an accurate representation of the physical properties of the fuel is a first important step, since spray formation is largely influenced by fuel properties such as viscosity, density, surface tension and vapour pressure. In the present work, a calculated biodiesel properties database based on the measured composition of Fatty Acid Methyl Esters (FAME) has been implemented in a multi-dimensional Computational Fluid Dynamics (CFD) spray simulation code. Simulations of non-reacting and reacting atmospheric-pressure sprays of both diesel and biodiesel have been carried out using a spray burner configuration for which experimental data is available. A pre-defined droplet size probability density function (pdf) has been implemented together with droplet dynamics based on phase Doppler anemometry (PDA) measurements in the near-nozzle region. The gas phase boundary condition for the reacting spray cases is similar to that of the experiment which employs a plain air-blast atomiser and a straight-vane axial swirler for flame stabilisation. A reaction mechanism for heptane has been used to represent the chemistry for both diesel and biodiesel. Simulated flame heights, spray characteristics and gas phase velocities have been found to compare well with the experimental results. In the reacting spray cases, biodiesel shows a smaller mean droplet size compared to that of diesel at a constant fuel mass flow rate. A lack of sensitivity towards different fuel properties has been observed based on the non-reacting spray simulations, which indicates a need for improved models of secondary breakup. By comparing the results of the non-reacting and reacting spray simulations, an improvement in the complexity of the physical modelling is achieved which is necessary in the understanding of the complex physical processes involved in spray combustion simulation. Copyright © 2012 SAE International.

Structuring technological information for technology roadmapping: Data mining approach

Most research on technology roadmapping has focused on its practical applications and the development of methods to enhance its operational process. Thus, despite a demand for well-supported, systematic information, little attention has been paid to how/which information can be utilised in technology roadmapping. Therefore, this paper aims at proposing a methodology to structure technological information in order to facilitate the process. To this end, eight methods are suggested to provide useful information for technology roadmapping: summary, information extraction, clustering, mapping, navigation, linking, indicators and comparison. This research identifies the characteristics of significant data that can potentially be used in roadmapping, and presents an approach to extracting important information from such raw data through various data mining techniques including text mining, multi-dimensional scaling and K-means clustering. In addition, this paper explains how this approach can be applied in each step of roadmapping. The proposed approach is applied to develop a roadmap of radio-frequency identification (RFID) technology to illustrate the process practically. © 2013 © 2013 Taylor & Francis.

Temperature dependence of hole spin relaxation in ultrathin InAs monolayers

The temperature dependence of hole spin relaxation time in both neutral and n-doped ultrathin InAs monolayers has been investigated. It has been suggested that D'yakonov-Perel (DP) mechanism dominates the spin relaxation process at both low and high temperature regimes. The appearance of a peak in temperature dependent spin relaxation time reveals the important contribution of Coulomb scatterings between carriers to the spin kinetics at low temperature, though electron-phonon scattering becomes dominant at higher temperatures. Increased electron screening effect in the n-doped sample has been suggested to account for the shortened spin relaxation time compared with the undoped one. The results suggest that hole spins are also promising for building solid-state qubits.

Formation of high reflective Ni/Ag/Ti/Au contact on p-GaN

A metallization scheme of Ni/Ag/Ti/Au has been developed for obtaining high reflective contacts on p-type GaN. In order to find optimal conditions to get a high reflectivity, we studied samples with various Ni thicknesses, annealing temperatures and annealing times. By annealing at 500 degrees C for 5 min in an O-2 ambient, a reflectivity as high as 94% was obtained from Ni/Ag/Ti/Au (1/120/120/50 nm). The effects of Ti layers on the suppression of Ag agglomeration were investigated by using Auger electron spectroscopy (AES). From AES depth profiles, it is clear that Ti acts as a diffusion barrier to prevent Au atoms from diffusing into the Ag layer, which is important in the formation of high reflectivity.

Quantum phase transitions in the S=1/2 distorted diamond chain

By means of the second derivative of the ground-state and first-excited energy, the quantum phase transitions (QPTs) for the distorted diamond chain (DDC) with ferromagnetic and antiferromagnetic frustrated interactions and the trimerized case are investigated, respectively. Our results show the plentiful quantum phases owing to the spin interaction competitions in the model. Meanwhile, by using the transfer-matrix renormalization-group technique, we study the two-site thermal entanglement of the DDC model in the thermodynamic limit for a further understanding of the QPTs.

Influence of Si doping on magnetic properties of (Ga,Mn)As

We have systematically investigated the magnetic properties of Si-doped (Ga,Mn)As films. When the Si content is low, both Curie temperature (T-C) and carrier density (p) decrease compared with undoped (Ga,Mn)As, whereas a monotonic increase of T-C and p is observed with further increase in the doping content of Si. We discuss the possible mechanism for the changes obtained by different Si doping contents and attribute the results to a competition between the existence of Si-Ga (Si substitutes for Ga site) that acts as a donor and Si-I (Si interstitials) which is in favor of the improvement of ferromagnetism. (C) 2008 Elsevier B.V. All rights reserved.

Spin states in semiconductor quantum dot with a single magnetic ion

We investigate theoretically CdTe quantum dots containing a single Mn2+ impurity, including the sp-d exchange interaction between carriers and the magnetic ion and the short-range exchange interaction between electron and hole. We find anticrossing behaviors in the energy spectrum of the electron-hole (e-h) pair that arise from the interplay between exchange interactions and the magnetic field. In addition to the s-d exchange interaction, we find that other mechanisms inducing the anticrossings become important in the strong heavy hole-light hole (hh-lh) mixing regime. The transition strengths between the states with spin projection of Mn2+ ion S-z not equal -5/2 (S-z = -5/2) decrease (increase) with increasing magnetic fields due to the alignment of the Mn2+ spin. The spin splitting of the e-h pair states depends sensitively on the external magnetic and electric field, which reveals useful information about the spin orientation and position of the magnetic ion. Meanwhile, the manipulation of the position of the magnetic ion offers us a way to control the spin splitting of the carriers. (C) 2008 Elsevier B.V. All rights reserved.

Mn-including InAs quantum dots fabricated by Mn implantation

Mn-including InAs quantum dots (QDs) were fabricated by Mn-ion implantation and subsequent annealing. The optical, compositional, and structural properties of the treated samples were analyzed by photoluminescence (PL) and microscopy. Energy dispersive X-ray (EDX) results indicate that Mn ions diffused from the bulk GaAs into the InAs QDs during annealing, and the diffusion appears to be driven by the strain in the InAs QDs. The temperature dependence of the PL of Mn-including InAs QD samples exhibits QDs PL characteristics. At the same time, the heavy Mn-including InAs QD samples have ferromagnetic properties and high T-c. (c) 2008 Elsevier B.V. All rights reserved.

Correlations between electronic energy bands spin splitting and magnetic profile symmetry of magnetic superlattice

We have theoretically investigated the energy band structures of two typical magnetic superlattices formed by perpendicular or parallel magnetization ferromagnetic stripes periodically deposited on a two-dimensional electron gas (2DEG), where the magnetic profile in the perpendicular magnetization is of inversion anti-symmetry, but of inversion symmetry in parallel magnetization, respectively. We have shown that the energy bands of perpendicular magnetization display the spin-splitting and transverse wave-vector symmetry, while the energy bands of the parallel magnetization exhibit spin degeneration and transverse wave-vector asymmetry. These distinguishing spin-dependent and transverse wave-vector asymmetry features are essential for future spintronics devices applications. (c) 2008 Elsevier B.V. All rights reserved.

Confined LO-phonon-assisted magnetotunneling in a parabolic quantum well with double barriers

The confined longitudinal-optical phonon-assisted tunneling through a parabolic quantum well with double barriers in a magnetic field perpendicular to the interfaces is studied theoretically based on a dielectric continuum model. The numerical results show that the applied magnetic field sharpens and heightens the phonon-assisted tunneling peaks in agreement with experimental observation. Furthermore, the phonon-assisted magnetotunneling peaks shift towards the higher biases as the magnetic field increases. In contrast to the results for a rectangular quantum well, the ratio of peak to valley of the phonon-assisted tunneling is larger for the wider well case. It also indicates that the phonon-assisted tunneling current peaks can be easily observed for a wider parabolic quantum well. (C) 2008 Published by Elsevier B.V.

Effects of accumulated strain on the surface and optical properties of stacked 1.3 mu m InAs/GaAs quantum dot structures

We report the effects of accumulated strain by stacking on the surface and optical properties of stacked 1.3 mu m InAs/GaAs quantum dot (QD) structures grown by MOCVD. It is found that the surface of the stacked QD structures becomes more and more undulated with stacking, due to the increased strain in the stacked QD structures with stacking. The photoluminescence intensity from the QD structures first increases as the stacking number increases from 1 to 3 and then dramatically decreases as it further increases, implying a significant increase in the density of crystal defects in the stacked QD structures due to the accumulated strain. Furthermore, we demonstrate that the strain can be reduced by simply introducing annealing steps just after growing the GaAs spacers during the deposition of the stacked QD structures, leading to significant improvement in the surface and optical properties of the structures. (C) 2007 Elsevier B.V. All rights reserved.

Temperature dependence of surface quantum dots grown under frequent growth interruption

We grow In-GaAs quantum dot (QD) at low growth rate with 70 times insertion of growth interruption in MBE system. It is found that because of the extreme growth condition, QDs exhibit a thick wetting layer, large QD height value and special surface morphology which is attributed to the In segregation effect. Temperature dependence of photoluminescence measurement shows that this kind of QDs has a good thermal stability which is explained in terms of a "group coupling" model put forward by us. (C) 2007 Elsevier B.V. All rights reserved.

Polarization dependence of absorption in strongly vertically coupled InAs/GaAs quantum dots for two-color far-infrared photodetector

Strongly vertically coupled InAs/GaAs quantum dots (QDs) with modulation doping are investigated, and polarization dependence of two-color absorptions was observed. Analysis of photoluminescence (PL) and absorption spectra shows that s-polarized absorptions at. 10.0 and 13.4 mu m, stem from the first excited state E-1 and the second excited state E-2 in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively, whereas p-polarized absorptions at 10.0 and 8.2 mu m stem from the first excited state E-1 and the ground E-g in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively. These measurements illustrate that transitions from excited states are more sensitive to normal incidence, which are very important in designing QD infrared detector. (C) 2007 Elsevier B.V. All rights reserved.