Approaches to reduce false positives and false negatives in the analysis of microarray data: applications in type 1 diabetes research

<p>Abstract</p> <p>Background</p> <p>As studies of molecular biology system attempt to achieve a comprehensive understanding of a particular system, Type 1 errors may be a significant problem. However, few investigators are inclined to accept the increase in Type 2 errors (false positives) that may result when less stringent statistical cut-off values are used. To address this dilemma, we developed an analysis strategy that used a stringent statistical analysis to create a list of differentially expressed genes that served as "bait" to "fish out" other genes with similar patterns of expression.</p> <p>Results</p> <p>Comparing two strains of mice (NOD and C57Bl/6), we identified 93 genes with statistically significant differences in their patterns of expression. Hierarchical clustering identified an additional 39 genes with similar patterns of expression differences between the two strains. Pathway analysis was then employed: 1) identify the central genes and define biological processes that may be regulated by the genes identified, and 2) identify genes on the lists that could not be connected to each other in pathways (potential false positives). For networks created by both gene lists, the most connected (central) genes were interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). These two cytokines are relevant to the biological differences between the two strains of mice. Furthermore, the network created by the list of 39 genes also suggested other biological differences between the strains.</p> <p>Conclusion</p> <p>Taken together, these data demonstrate how stringent statistical analysis, combined with hierarchical clustering and pathway analysis may offer deeper insight into the biological processes reflected from a set of expression array data. This approach allows us to 'recapture" false negative genes that otherwise would have been missed by the statistical analysis.</p

Disability interactions in digital games: From accessibility to inclusion

Digital games are a hugely popular activity enjoyed for the diverse experiences and relationships that they offer players. In 2019, games are more accessible to an increasingly diverse audience of disabled players through both new gaming technology and in-game options that allow people to tune their experiences. As a significant cultural medium, it is also challenging perceptions of disability in how characters are depicted. In this workshop, we aim to understand better the research challenges in making games for and with disabled players. We explore opportunities in games and disability through the lens of the new Disability Interaction (DIX) manifesto

Deterministic and Stochastic Spin Diffusion in Classical Heisenberg Magnets

This computer simulation study provides further evidence that spin diffusion in the one‐dimensional classical Heisenberg model at T=∞ is anomalous: 〈S j ( t )⋅S j 〉 ∼t −α 1 withα1 ≳1/2. However, the exponential instability of the numerically integrated phase‐space trajectories transforms the deterministic transport of spin fluctuations into a computationally generated stochastic process in which the global conservation laws are still satisfied to high precision. This may cause a crossover in 〈S j ( t )⋅S j 〉 from anomalous spin diffusion (α1 ≳ 1/2) to normal spin diffusion (α1 = 1/2) at some characteristic time lag that depends on the precision of the numerical integration

A Simulation Study of the Factors Influencing the Risk of Intraoperative Slipping

AbstractBackgroundTo identify the impact of weight, table surface, and table type on slipping in a simulation of minimally invasive gynecologic surgery.MethodsA mannequin was placed into increasing Trendelenburg until a slip was observed; the table angle at the time of the event was measured (slip angle). The influence of mannequin position (supine vs. lithotomy), weight, table surface, and model was evaluated. A linear regression model was used to analyze the data.ResultsMannequin weight, bed surface, and bed type all significantly impacted the slip angles. In general, higher mannequin weights tolerated significantly more Trendelenburg before slipping in the supine position but less in lithotomy compared to lower weights. In lithotomy, the disposable sheet and gelpad performed worse than the bean bag, egg crate foam, and bedsheet. There was no difference in slipping because of bed surface in the supine model. The Skytron operating table performed significantly better than the Steris operating table when tested with the bedsheet.ConclusionOperative position, patient weight, and bed surface together influence the slipping propensity. In lithotomy, heavier patients were more prone to slipping while the inverse was true in supine. The egg crate foam, bean bag, and bedsheet were the best antislip surfaces. Operating room table choice can mitigate slippage

Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases

We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include histograms of subphases. The free energy difference between phases, necessary for attributing the correct statistical weights to the histograms, is determined by a detour in control parameter space via auxiliary systems with short relaxation times. We apply this method to a recently introduced model for structure formation in polypeptides for which other methods fail.Comment: 13 pages in preprint mode, REVTeX, 2 Figures available from the authors ([email protected], [email protected]

Creating wheelchair-controlled video games: challenges and opportunities when involving young people with mobility impairments and game design experts

Although participatory design (PD) is currently the most acceptable and respectful process we have for designing technology, recent discussions suggest that there may be two barriers to the successful application of PD to the design of digital games: First, the involvement of audiences with special needs can introduce new practical and ethical challenges to the design process. Second, the use of non-experts in game design roles has been criticised in that participants lack skills necessary to create games of appropriate quality. To explore how domain knowledge and user involvement influence game design, we present results from two projects that addressed the creation of movement-based wheelchair-controlled video games from different perspectives. The first project was carried out together with a local school that provides education for young people with special needs, where we invited students who use wheelchairs to take part in design sessions. The second project involved university students on a game development course, who do not use wheelchairs, taking on the role of expert designers. They were asked to design concepts for wheelchair-controlled games as part of a final-year course on game design. Our results show that concepts developed by both groups were generally suitable examples of wheelchair-controlled motion-based video games, but we observed differences regarding level of detail of game concepts, and ideas of disability. Additionally, our results show that the design exercise exposed vulnerabilities in both groups, outlining that the risk of practical and emotional vulnerability needs to be considered when working with the target audience as well as expert designers