Assessment Method for a Power Analysis to Identify Differentially Expressed Pathways

Gene expression data can provide a very rich source of information for elucidating the biological function on the pathway level if the experimental design considers the needs of the statistical analysis methods. The purpose of this paper is to provide a comparative analysis of statistical methods for detecting the differentially expression of pathways (DEP). In contrast to many other studies conducted so far, we use three novel simulation types, producing a more realistic correlation structure than previous simulation methods. This includes also the generation of surrogate data from two large-scale microarray experiments from prostate cancer and ALL. As a result from our comprehensive analysis of 41,004 parameter configurations, we find that each method should only be applied if certain conditions of the data from a pathway are met. Further, we provide method-specific estimates for the optimal sample size for microarray experiments aiming to identify DEP in order to avoid an underpowered design. Our study highlights the sensitivity of the studied methods on the parameters of the system. © 2012 Tripahti and Emmert-Streib.

Numerical analysis of intralaminar failure mechanisms in composite structures, Part I: FE implementation

This paper presents a three-dimensional continuum damage mechanics-based material model which was implemented in an implicit finite element code to simulate the progressive intralaminar degradation of fibre reinforced laminates. The damage model is based on ply failure mechanisms and uses seven damage variables assigned to tensile, compressive and shear damage at a ply level. Non-linear behaviour and irreversibility were taken into account and modelled. Some issues on the numerical implementation of the damage model are discussed and solutions proposed. Applications of the methodology are presented in Part II

Numerical analysis of intralaminar failure mechanisms in composite structures, Part II: Applications

A three-dimensional continuum damage mechanics-based material model was implemented in an implicit Finite Element code to simulate the progressive intralaminar degradation of fibre reinforced laminates based on ply failure mechanisms. This paper presents some structural applications of the progressive failure model implemented. The focus is on the non-linear response of the shear failure mode and its interaction with other failure modes. Structural applications of the damage model show that the proposed model is able to reproduce failure loads and patterns observed experimentally.

Analysis of Betaine and Choline Contents of Aleurone, Bran, and Flour Fractions of Wheat (Triticum aestivum L.) Using 1H Nuclear Magnetic Resonance (NMR) Spectroscopy

In conventional milling, the aleurone layer is combined with the bran fraction. Studies indicate that the bran fraction of wheat contains the majority of the phytonutrients betaine and choline, with relatively minor concentrations in the refined flour. This present study suggests that the wheat aleurone layer (Triticum aestivum L. cv. Tiger) contains the greatest concentration of both betaine and choline (1553.44 and 209.80 mg/100 g of sample, respectively). The bran fraction contained 866.94 and 101.95 mg/100 g of sample of betaine and choline, respectively, while the flour fraction contained 23.30 mg/100 g of sample (betaine) and 28.0 mg/100 g of sample (choline). The betaine content for
the bran was lower, and the choline content was higher compared to previous studies, although it is known that there is large variation in betaine and choline contents between wheat cultivars. The ratio of betaine/choline in the aleurone fraction was approximately 7:1; in the bran, the ratio was approximately 8:1; and in the flour fraction, the ratio was approximately 1:1. The study further
emphasizes the superior phytonutrient composition of the aleurone layer.
INTRODUCTION
Wheat is a valuable source of betaine, choline (1, 2), B
vitamins, vitamin E, and a number of minerals, including iron,
zinc, magnesium, and phosphorus (3). Epidemiological studies
indicate that whole-grain consumption is protective against
several chronic diseases (4-12). It has not been fully elucidated
how whole-grain cereals or specific fractions (13) exert their
protective effect, but it is thought to be due to their content of
several nutrients associated with the reduced risk of disease.
Conventionally, whole grain is separated during milling into
bran, germ, and flour (14). The nutrient composition of these
fractions differ markedly; refined wheat flour contains approximately
50% less vitamins and minerals than whole-grain
flour (

The Source of 3 Minute Magnetoacoustic Oscillations in Coronal Fans

We use images of high spatial, spectral, and temporal resolution, obtained using both ground- and space-based instrumentation, to investigate the coupling between wave phenomena observed at numerous heights in the solar atmosphere. Analysis of 4170 Å continuum images reveals small-scale umbral intensity enhancements, with diameters ~0."6, lasting in excess of 30 minutes. Intensity oscillations of ˜3 minutes are observed to encompass these photospheric structures, with power at least three orders of magnitude higher than the surrounding umbra. Simultaneous chromospheric velocity and intensity time series reveal an 87?±8? out-of-phase behavior, implying the presence of standing modes created as a result of partial wave re?ection at the transition region boundary. We ?nd a maximum waveguide inclination angle of˜40? between photospheric and chromospheric heights, combined with a radial expansion factor of <76%. An average blueshifted Doppler velocity of ˜1.5 km s-1, in addition to a time lag between photospheric and chromospheric oscillatory phenomena, con?rms the presence of upwardly propagating slow-mode waves in the lower solar atmosphere. Propagating oscillations in EUV intensity are detected in simultaneous coronal fan structures, with a periodicity of 172±17 s and a propagation velocity of 45±7 km s-1. Numerical simulations reveal that the damping of the magnetoacoustic wave trains is dominated by thermal conduction. The coronal fans are seen to anchor into the photosphere in locations where large-amplitude umbral dot (UD) oscillations manifest. Derived kinetic temperature and emission measure time series display prominent outof-phase characteristics, and when combined with the previously established sub-sonic wave speeds, we conclude that the observed EUV waves are the coronal counterparts of the upwardly propagating magnetoacoustic slow modes detected in the lower solar atmosphere. Thus, for the ?rst time, we reveal how the propagation of 3 minute magnetoacoustic waves in solar coronal structures is a direct result of amplitude enhancements occurring in photospheric UDs.photospheric UDs.

The use of ensemble empirical mode decomposition with canonical correlation analysis as a novel artifact removal technique

Biosignal measurement and processing is increasingly being deployed in ambulatory situations particularly in connected health applications. Such an environment dramatically increases the likelihood of artifacts which can occlude features of interest and reduce the quality of information available in the signal. If multichannel recordings are available for a given signal source, then there are currently a considerable range of methods which can suppress or in some cases remove the distorting effect of such artifacts. There are, however, considerably fewer techniques available if only a single-channel measurement is available and yet single-channel measurements are important where minimal instrumentation complexity is required. This paper describes a novel artifact removal technique for use in such a context. The technique known as ensemble empirical mode decomposition with canonical correlation analysis (EEMD-CCA) is capable of operating on single-channel measurements. The EEMD technique is first used to decompose the single-channel signal into a multidimensional signal. The CCA technique is then employed to isolate the artifact components from the underlying signal using second-order statistics. The new technique is tested against the currently available wavelet denoising and EEMD-ICA techniques using both electroencephalography and functional near-infrared spectroscopy data and is shown to produce significantly improved results. © 1964-2012 IEEE.

Finite Element Analysis of Drilling of Carbon Fibre Reinforced Composites

Despite the increased applications of the composite materials in aerospace due to their exceptional physical and mechanical properties, the machining of composites remains a challenge. Fibre reinforced laminated composites are prone to different damages during machining process such as delamination, fibre pull-out, microcracks, thermal damages. Optimization of the drilling process parameters can reduces the probability of these damages. In the current research, a 3D finite element (FE) model is developed of the process of drilling in the carbon fibre reinforced composite (CFC). The FE model is used to investigate the effects of cutting speed and feed rate on thrust force, torque and delamination in the drilling of carbon fiber reinforced laminated composite. A mesoscale FE model taking into account of the different oriented plies and interfaces has been proposed to predict different damage modes in the plies and delamination. For validation purposes, experimental drilling tests have been performed and compared to the results of the finite element analysis. Using Matlab a digital image analysis code has been developed to assess the delamination factor produced in CFC as a result of drilling. © Springer Science+Business Media B.V. 2011.

Analysis of Fixed-Speed Wind Farm Low-Frequency Power Pulsations using a Wavelet-Prony Method

The increasing penetration of wind generation on the Island of Ireland has been accompanied by close investigation of low-frequency periodic pulsations contained within the active power flow from different wind farms. A primary concern is excitation of existing low-frequency oscillation modes already present on the system, particularly the 0.75 Hz mode as a consequence of the interconnected Northern and Southern power system networks. Recently grid code requirements on the Northern Ireland power system have been updated stipulating that wind farms connected after 2005 must be able to control the magnitude of oscillations in the range of 0.25 - 1.75 Hz to within 1% of the wind farm's registered output. In order to determine whether wind farm low-frequency oscillations have a negative effect (excite other modes) or possibly a positive impact (damping of existing modes) on the power system, the oscillations at the point of connection must be measured and characterised. Using time - frequency methods, research presented in this paper has been conducted to extract signal features from measured low-frequency active power pulsations produced by wind farms to determine the effective composition of possible oscillatory modes which may have a detrimental effect on system dynamic stability. The paper proposes a combined wavelet-Prony method to extract modal components and determine damping factors. The method is exemplified using real data obtained from wind farm measurements.

Analysis of Dependence Tracking Algorithms for Task Dataflow Execution

Processor architectures has taken a turn towards many-core processors, which integrate multiple processing cores on a single chip to increase overall performance, and there are no signs that this trend will stop in the near future. Many-core processors are harder to program than multi-core and single-core processors due to the need of writing parallel or concurrent programs with high degrees of parallelism. Moreover, many-cores have to operate in a mode of strong scaling because of memory bandwidth constraints. In strong scaling increasingly finer-grain parallelism must be extracted in order to keep all processing cores busy.

Task dataflow programming models have a high potential to simplify parallel program- ming because they alleviate the programmer from identifying precisely all inter-task de- pendences when writing programs. Instead, the task dataflow runtime system detects and enforces inter-task dependences during execution based on the description of memory each task accesses. The runtime constructs a task dataflow graph that captures all tasks and their dependences. Tasks are scheduled to execute in parallel taking into account dependences specified in the task graph.

Several papers report important overheads for task dataflow systems, which severely limits the scalability and usability of such systems. In this paper we study efficient schemes to manage task graphs and analyze their scalability. We assume a programming model that supports input, output and in/out annotations on task arguments, as well as commutative in/out and reductions. We analyze the structure of task graphs and identify versions and generations as key concepts for efficient management of task graphs. Then, we present three schemes to manage task graphs building on graph representations, hypergraphs and lists. We also consider a fourth edge-less scheme that synchronizes tasks using integers. Analysis using micro-benchmarks shows that the graph representation is not always scalable and that the edge-less scheme introduces least overhead in nearly all situations.

What the newspapers say about medication adherence: a content analysis

Background: This study investigates the coverage of adherence to medicine by the UK and US newsprint media. Adherence to medicine is recognised as an important issue facing healthcare professionals and the newsprint media is a key source of health information, however, little is known about newspaper coverage of medication adherence.

Methods. A search of the newspaper database Nexis®UK from 2004-2011 was performed. Content analysis of newspaper articles which referenced medication adherence from the twelve highest circulating UK and US daily newspapers and their Sunday equivalents was carried out. A second researcher coded a 15% sample of newspaper articles to establish the inter-rater reliability of coding.

Results: Searches of newspaper coverage of medication adherence in the UK and US yielded 181 relevant articles for each country. There was a large increase in the number of scientific articles on medication adherence in PubMed® over the study period, however, this was not reflected in the frequency of newspaper articles published on medication adherence. UK newspaper articles were significantly more likely to report the benefits of adherence (p = 0.005), whereas US newspaper articles were significantly more likely to report adherence issues in the elderly population (p = 0.004) and adherence associated with diseases of the central nervous system (p = 0.046). The most commonly reported barriers to adherence were patient factors e.g. poor memory, beliefs and age, whereas, the most commonly reported facilitators to adherence were medication factors including simplified regimens, shorter treatment duration and combination tablets. HIV/AIDS was the single most frequently cited disease (reported in 20% of newspaper articles). Poor quality reporting of medication adherence was identified in 62% of newspaper articles.

Conclusion: Adherence is not well covered in the newspaper media despite a significant presence in the medical literature. The mass media have the potential to help educate and shape the public's knowledge regarding the importance of medication adherence; this potential is not being realised at present. © 2013 Goodfellow et al.; licensee BioMed Central Ltd.

Automated detection and measurement of isolated retinal arterioles by a combination of edge enhancement and cost analysis

Pressure myography studies have played a crucial role in our understanding of vascular physiology and pathophysiology. Such studies depend upon the reliable measurement of changes in the diameter of isolated vessel segments over time. Although several software packages are available to carry out such measurements on small arteries and veins, no such software exists to study smaller vessels (<50 µm in diameter). We provide here a new, freely available open-source algorithm, MyoTracker, to measure and track changes in the diameter of small isolated retinal arterioles. The program has been developed as an ImageJ plug-in and uses a combination of cost analysis and edge enhancement to detect the vessel walls. In tests performed on a dataset of 102 images, automatic measurements were found to be comparable to those of manual ones. The program was also able to track both fast and slow constrictions and dilations during intraluminal pressure changes and following application of several drugs. Variability in automated measurements during analysis of videos and processing times were also investigated and are reported. MyoTracker is a new software to assist during pressure myography experiments on small isolated retinal arterioles. It provides fast and accurate measurements with low levels of noise and works with both individual images and videos. Although the program was developed to work with small arterioles, it is also capable of tracking the walls of other types of microvessels, including venules and capillaries. It also works well with larger arteries, and therefore may provide an alternative to other packages developed for larger vessels when its features are considered advantageous.

Job strain and the risk of severe asthma exacerbations: A meta-analysis of individual-participant data from 100 000 European men and women

Background: Many patients and healthcare professionals believe that work-related psychosocial stress, such as job strain, can make asthma worse, but this is not corroborated by empirical evidence. We investigated the associations between job strain and the incidence of severe asthma exacerbations in working-age European men and women. Methods: We analysed individual-level data, collected between 1985 and 2010, from 102 175 working-age men and women in 11 prospective European studies. Job strain (a combination of high demands and low control at work) was self-reported at baseline. Incident severe asthma exacerbations were ascertained from national hospitalization and death registries. Associations between job strain and asthma exacerbations were modelled using Cox regression and the study-specific findings combined using random-effects meta-analyses. Results: During a median follow-up of 10 years, 1 109 individuals experienced a severe asthma exacerbation (430 with asthma as the primary diagnostic code). In the age- and sex-adjusted analyses, job strain was associated with an increased risk of severe asthma exacerbations defined using the primary diagnostic code (hazard ratio, HR: 1.27, 95% confidence interval, CI: 1.00, 1.61). This association attenuated towards the null after adjustment for potential confounders (HR: 1.22, 95% CI: 0.96, 1.55). No association was observed in the analyses with asthma defined using any diagnostic code (HR: 1.01, 95% CI: 0.86, 1.19). Conclusions: Our findings suggest that job strain is probably not an important risk factor for severe asthma exacerbations leading to hospitalization or death.

Two-Way Relaying Networks with Wireless Power Transfer: Policies Design and Throughput Analysis

This paper exploits an amplify-and-forward (AF) two-way relaying network (TWRN), where an energy constrained relay node harvests energy with wireless power transfer. Two bidirectional protocols, multiple access broadcast (MABC) protocol and time division broadcast (TDBC) protocol, are considered. Three wireless power transfer policies, namely, 1) dual-source (DS) power transfer; 2) single-fixed-source (SFS) power transfer; and 3) single-best-source (SBS) power transfer are proposed and well-designed based on time switching receiver architecture. We derive analytical expressions to determine the throughput both for delay-limited transmission and delay-tolerant transmission. Numerical results corroborate our analysis and show that MABC protocol achieves a higher throughput than TDBC protocol. An important observation is that SBS policy offers a good tradeoff between throughput and power.

Analysis of VSC-based HVDC System under DC Faults

This paper analyzes the behavior of a Voltage Source Converter Based HVDC system under DC cable fault conditions. The behavior of the HVDC system during a permanent line-to-earth fault is analyzed, outlining the systems configuration and behavior at each stage of the fault timeline. Operation of the proposed system under a single earthing configurations i.e. Converter (solid) earthed/AC transformer unearthed, was analyzed and simulated, with particular attention paid to the converters operation. It was observed that the development of potential earth loops within the system as a result of DC line- toearth faults leads to substantial overcurrent and results in system configuration oscillation.