Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets

Motivation: To date, Gene Set Analysis (GSA) approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods for identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations, or other pairwise measures of coexpression. Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes.

Results: In GSNCA, weight factors are assigned to genes in proportion to the genes' cross-correlations (intergene correlations). The problem of finding the weight vectors is formulated as an eigenvector problem with a unique solution. GSNCA tests the null hypothesis that for a gene set there is no difference in the weight vectors of the genes between two conditions. In simulation studies and the analyses of experimental data, we demonstrate that GSNCA, indeed, captures changes in the structure of genes' cross-correlations rather than differences in the averaged pairwise correlations. Thus, GSNCA infers differences in coexpression networks, however, bypassing method-dependent steps of network inference. As an additional result from GSNCA, we define hub genes as genes with the largest weights and show that these genes correspond frequently to major and specific pathway regulators, as well as to genes that are most affected by the biological difference between two conditions. In summary, GSNCA is a new approach for the analysis of differentially coexpressed pathways that also evaluates the importance of the genes in the pathways, thus providing unique information that may result in the generation of novel biological hypotheses.

Detectability of bovine TB using the tuberculin skin test does not vary significantly according to pathogen genotype within Northern Ireland

Strains of many infectious diseases differ in parameters that influence epidemic spread, for example virulence, transmissibility, detectability and host specificity. Knowledge of inter-strain variation can be exploited to improve management and decrease disease incidence. Bovine tuberculosis (bTB) is increasingly prevalent among farmed cattle in the UK, exerting a heavy economic burden on the farming industry and government. We aimed to determine whether strains of Mycobacterium bovis (the causative agent of bTB) identified and classified using genetic markers (spoligotyping and multi-locus VNTR analysis) varied in response to the tuberculin skin test; this being the primary method of bTB detection used in the UK. Inter-strain variation in detectability of M. bovis could have important implications for disease control. The skin test is based on a differential delayed type hypersensitivity (DTH) response to intradermal injections of purified protein derivative (PPD) from M. bovis (PPD-B) and Mycobacterium avium (PPD-A). We searched for an association between skin test response (PPD-B skin rise minus PPD-A skin rise) and M. bovis genotype at the disclosing test in culture-confirmed cases using a field dataset consisting of 21,000 isolates belonging to 63 genotypes of M. bovis from cattle in Northern Ireland. We found no substantial variation among genotypes (estimated responses clustered tightly around the mean) controlling for animal sex, breed and test effects. We also estimated the ratio of skin test detected to undetected cases (i.e. cases only detected at abattoir). The skin test detection ratio varied among abattoirs with some detecting a greater proportion of cases than others but this variation was unrelated to the community composition of genotypes within each abattoir catchment. These two lines of evidence indicate that M. bovis genotypes in Northern Ireland have similar detectability using the skin test.

A static test method to assess swivel seat strength in frontal impact

Mechanical swivel seat adaptations are a key aftermarket disability modification to any small-to medium-sized passenger vehicle. However, the crashworthiness of these devices is currently unregulated and the existing 20g dynamic sled testing approach is prohibitively expensive for prototype assessment purposes. In this paper, an alternative quasi-static test method for swivel seat assessment is presented, and two different approaches (free-body diagram and multibody modelling) validated through published experimental data are developed to determine the appropriate loading conditions to apply in the quasi-static testing.Results show the two theoretical approaches can give similar results for estimating the quasi-static loading conditions, and this depends on the seatbelt configuration. Application of the approach to quasi-static testing of both conventional seats and those with integrated seat belts showed the approach to be successful and easy to apply. It is proposed that this method be used by swivel seat designers to assess new prototypes prior to final validation via the traditional 20g sled test.

Evaluation of Corrosion Fatigue Behaviour of Laser-welded NiTi Alloys using Bending Rotation Fatigue Test in Simulated Body Fluid

Shape memory NiTi alloys have been used extensively for medical device applications such as orthopedic, dental, vascular and cardiovascular devices on account of their unique shape memory effect (SME) and super-elasticity (SE). Laser welding is found to be the most suitable method used to fabricate NiTi-based medical components. However, the performance of laser-welded NiTi alloys under corrosive environments is not fully understood and a specific focus on understanding the corrosion fatigue behaviour is not evident in the literature. This study reveals a comparison of corrosion fatigue behaviour of laser-welded and bare NiTi alloys using bending rotation fatigue (BRF) test which was integrated with a specifically designed corrosion cell. The testing environment was Hanks’ solution (simulated body fluid) at 37.5oC. Electrochemical impedance spectroscopic (EIS) measurement was carried out to monitor the change of corrosion resistance at different periods during the BRF test. Experiments indicate that the laser-welded NiTi alloy would be more susceptible to the corrosion fatigue attack than the bare NiTi alloy. This finding can serve as a benchmark for the product designers and engineers to determine the factor of safety of NiTi medical devices fabricated using laser welding.

Synergy Between an Improved Covariate Unit Root Test and Cross-sectionally Dependent Panel Data Unit Root Tests, with two Applications

This paper proposes the use of an improved covariate unit root test which exploits the cross-sectional dependence information when the panel data null hypothesis of a unit root is rejected. More explicitly, to increase the power of the test, we suggest the utilization of more than one covariate and offer several ways to select the ‘best’ covariates from the set of potential covariates represented by the individuals in the panel. Employing our methods, we investigate the Prebish-Singer hypothesis for nine commodity prices. Our results show that this hypothesis holds for all but the price of petroleum.

The Effect of the Secret Ballot on Party System Fragmentation: A Test of Three Competing Arguments

Few studies have examined the impact that the adoption of the secret ballot had on party system fragmentation outside the United States. This article tests arguments maintaining that the adoption of the secret ballot had a negative, positive or nil effect on party system fragmentation. Using time-series cross-sectional data from
several countries adopting the secret ballot around the turn of the twentieth century, the results demonstrate that the adoption of the secret ballot did not hinder – though did not favour, either – the development of multiparty systems.

Conductivity sensor technology application in steady state migration test

In this paper the current development of the steady state migration test was reviewed. Experiments were carried out for a series of concrete mixes with the steady state migration test in which conductivity sensor technology is applied. With the developed steady state migration test, conductivity in anolyte, loop current and temperature can be monitored in real time. The experimental results are conductive to understand the mechanism of chloride migration during both unsteady state and steady state. The conductivity of anolyte could be used to calculate the chloride concentration in anolyte and the theoretical correlation between them was explained. Over all, the developed steady state migration is an effective, convenient, well-defined in theory and plentiful with information method which could be used to determine the chloride diffusion coefficient of cementitious materials.

Proportionality in Age Discrimination Cases - a Model Suitable for Socially Embedded Rights

This chapter discusses the use of proportionality in age discrimination cases before the Court of Justice of the European Union. It argues that the Court does not use this concept systematically - indeed it exposes some contradiction that make the case law seem arbitrary - and proposes a more fruitful use of the principle, which is in line with a modern conception of human rights. The chapter argues that the principle of proportionality stems from the time when human rights served the recently liberated burgeois elite in guarding their rights to property and liberty against the state. Today, states not only respect human rights (which is fully sufficient for this elite, who can rely on their inherited wealth to fend for themselves). They also protect and promote human rights, and these activities are a precondition for human rights to be practically relevant for the whole population. This also means that state activity, which is experienced as a limitation of rights to property and liberty by some, may constitute a measure to promote and protect human rights of others. In employment law - the only field where the EU ban on age discrimination is applied - this is a typical situation. If such a situation occurs, the principle of proportionality must be applied in a bifurcated way.It is not sufficient that the limitation of property rights is proportionate for the achievement of a public policy aim. If the aim of public policy is to enable the effective use of human rights, the limitation of the state action must be proportionate to the protection and promotion of those human rights. It is argued that the principle of proportionality is superior to less structures balancing acts (e.g. the Wednesbury principle), if it is applied both ways. Going over to the field of age discrimination, the chapter identifies a number of potentially colliding aims pursued in this field. Banning age discrimination may relate to genuine aims of anti-discrimination law if bias against older or very young workers is addressed. However, the EU ban of discrimination against all ages also serves to restructure employment law and policy to the age of flexibilisation, replacing the synchronisation principle that has been predominant for the welfare states of the 20th century. The former aim is related to human rights protection, while the latter aim is not (at least not always). This has consequences for applying the proportionality test. The chapter proposes different ways to argue the most difficult age discrimination cases, where anti-discrimination rationales and flexibilisation rationales clash

Vehicle-barrier tracking of a scaled crash test for roadside barrier design

In this paper the tracking system used to perform a scaled vehicle-barrier crash test is reported. The scaled crash test was performed as part of a wider project aimed at designing a new safety barrier making use of natural building materials. The scaled crash test was designed and performed as a proof of concept of the new mass-based safety barriers and the study was composed of two parts: the scaling technique and of a series of performed scaled crash tests. The scaling method was used for 1) setting the scaled test impact velocity so that energy dissipation and momentum transferring, from the car to the barrier, can be reproduced and 2) predicting the acceleration, velocity and displacement values occurring in the full-scale impact from the results obtained in a scaled test. To achieve this goal the vehicle and barrier displacements were to be recorded together with the vehicle accelerations and angular velocities. These quantities were measured during the tests using acceleration sensors and a tracking system. The tracking system was composed of a high speed camera and a set of targets to measure the vehicle linear and angular velocities. A code was developed to extract the target velocities from the videos and the velocities obtained were then compared with those obtained integrating the accelerations provided by the sensors to check the reliability of the method.

Associations between Achievement Goal Orientations and Academic Performance Among Students at a UK Pharmacy School

Objective. To ascertain goal orientations of pharmacy students and establish whether associations exist between academic performance, gender, or year of study. Methods. Goal orientations were assessed using a validated questionnaire. Respondents were categorized as high or low performers based on university grades. Associations and statistical significance were ascertained using parametric and nonparametric tests and linear regression, as appropriate. Results. A response rate of 60.7% was obtained. High performers were more likely to be female than male. The highest mean score was for mastery approach; the lowest for work avoidance. The mean score for work avoidance was significantly greater for low performers than for high performers and for males than for females. First-year students were most likely to have top scores in mastery and performance approaches. Conclusion. It is encouraging that the highest mean score was for mastery approach orientation, as goal orientation may play a role in academic performance of pharmacy students.

The performance of concrete exposed to marine environments: predictive modelling and use of laboratory/on site test methods

This paper reports an approach by which laboratory based testing and numerical modelling can be combined to predict the long term performance of a range of concretes exposed to marine environments. Firstly, a critical review of the test methods for assessing the chloride penetration resistance of concrete is given. The repeatability of the different test results is also included. In addition to the test methods, a numerical simulation model is used to explore the test data further to obtain long-term chloride ingress trends. The combined use of testing and modelling is validated with the help of long-term chloride ingress data from a North Sea exposure site. In summary, the paper outlines a methodology for determining the long term performance of concrete in marine environments.

Do mirrors reflect reality in agonistic encounters? A test of mutual cooperation in displays

Animals frequently engage in mutual displays that may allow or at least help decisions about the outcome of agonistic encounters with mutual benefit to the opponents. In fish these often involve lateral displays, with previous studies finding evidence of population-level lateralization with a marked preference for showing the right side and using the right eye. Because both opponents tend to show this preference a head to tail configuration is formed and is used extensively during the display phase. Here we tested the significance of these lateral displays by comparing displays to a mirror with those to a real opponent behind a transparent barrier. The frequency of displays was lower to a mirror but the individual displays were of greater duration indicating a slower pace of the interaction with a mirror. This suggests that fish respond to initiatives of real opponents but as mirror images do not initiate moves the focal fish only moves when it is ready to change position. However, lateralization was still found with mirrors, indicating that the right-side bias is a feature of the individual and not of the interaction between opponents. We discuss implications for ideas about the evolution of mutual cooperation and information exchange in contests, as well as the utility of the use of mirrors in the study of aggression in fish.