Finding function: evaluation methods for functional genomic data

BACKGROUND: Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. There is currently no standard approach to evaluation in functional genomics. Our analysis of existing approaches shows that they are inconsistent and contain substantial functional biases that render the resulting evaluations misleading both quantitatively and qualitatively. These problems make it essentially impossible to compare computational methods or large-scale experimental datasets and also result in conclusions that generalize poorly in most biological applications. RESULTS: We reveal issues with current evaluation methods here and suggest new approaches to evaluation that facilitate accurate and representative characterization of genomic methods and data. Specifically, we describe a functional genomics gold standard based on curation by expert biologists and demonstrate its use as an effective means of evaluation of genomic approaches. Our evaluation framework and gold standard are freely available to the community through our website. CONCLUSION: Proper methods for evaluating genomic data and computational approaches will determine how much we, as a community, are able to learn from the wealth of available data. We propose one possible solution to this problem here but emphasize that this topic warrants broader community discussion

An examination of the clinical outcomes of adolescents and young adults with broad autism spectrum traits and autism spectrum disorder and anorexia nervosa: A multi centre study

Objectives: To compare the clinical outcomes of adolescents and young adults with anorexia nervosa (AN) comorbid with broad autism spectrum disorder (ASD) or ASD traits. Method: The developmental and well‐being assessment and social aptitude scale were used to categorize adolescents and young adults with AN (N = 149) into those with ASD traits (N = 23), and those who also fulfilled diagnostic criteria for a possible/probable ASD (N = 6). We compared both eating disorders specific measures and broader outcome measures at intake and 12 months follow‐up. Results: Those with ASD traits had significantly more inpatient/day‐patient service use (p = .015), as well as medication use (p < .001) at baseline. Both groups had high social difficulties and poorer global functioning (strengths and difficulties questionnaire) at baseline, which improved over time but remained higher at 12 months in the ASD traits group (p = .002). However, the improvement in eating disorder symptoms at 12 months was similar between groups with or without ASD traits. Treatment completion rates between AN only and ASD traits were similar (80.1 vs. 86.5%). Discussion: Adolescents with AN and ASD traits show similar reductions in their eating disorder symptoms. Nevertheless, their social difficulties remain high suggesting that these are life‐long difficulties rather than starvation effects

Partisan Views of the Economy

In this paper it is argued that political parties may have incentives to adopt a partisan view on the working of the economic system. Our approach is based on a dynamical spatial voting model in which political parties are policy oriented. This model revolves around two interrelated issues x and y. The policy maker sets x directly. There exist two views on the relationship between x and y. Model uncertainty confronts policy makers with the problem of the selection of a model to base their actions on. We show that if voters have imperfect information about the working of the economic system that model selection contains a strategic element. Policy makers are inclined to adopt a view on the working of the economic system which fits in with their preferences. There is no inherent logic that places monetarists to the right of New Economists. They have different models of economic mechanism, but they need not have different political values. A conservative can be a Keynesian and a liberal a monetarist. These combinations are in fact surprisingly rare. James Tobin, 1974,The New Economics One Decade Older, p. 62. I am greatly indebted to Peter Broer, Ben Heydra, Jos Jansen and Wilko Letterie for many helpful suggestions. Furthermore, I would like to thank an anonymous referee for his comments

Neutral beam injector oxygen impurity measurements and concentration reduction via gettering processes. Revision 1

We have measured the reduction of oxygen impurity levels by means of gettering within the arc chambers of the TMX-U neutral-beam injectors using the TMX-U neutral-beam test stand. Our analysis incorporated silicon surface-probe measurements and optical Doppler-shift measurements of the hydrogen alpha spectra of deuterium atoms with energies appropriate for D/sub 2/O parentage. Without gettering, the Auger electron spectroscopy analysis of an exposed silicon sample showed a large oxygen peak below the surface peak with a concentration equivalence of approximately 2% for an accelerated beam. After gettering, with either titanium or chromium getters, optical monochromator data indicated a reduction in the oxygen concentration of at least a factor of 10 whereas Auger spectroscopy data showed at least a factor-of-eight reduction. Other metallic impurities remained below the level of detection even after gettering. Additional effects observed during this study include a change in the accelerated deuterium species concentrations, loss of gettering activity, loss of arc operation, and a change in arc performance due to arc chamber gas absorption during operation

Neutral beam injector oxygen impurity measurements and concentration reduction via gettering processes

The reduction of oxygen impurity levels by means of gettering within the arc chambers of the TMX-U neutral beam injectors has been measured. The TMX-U Neutral Beam Test Stand was used for this experiment. Analysis incorporated silicon surface probes and optical Doppler-shift measurements of the Lyman alpha spectra of deuterium atoms with energies appropriate for D/sub 2/O parentage. Without gettering, the Auger electron spectroscopy analysis of an exposed silicon sample showed a large oxygen peak below the surface peak with a concentration equivalent of approximately 2% for an accelerated beam. After gettering, with either titanium or chromium getters, the oxygen concentration was reduced by at least a factor of 10 according to optical monochromator data, and at least a factor of 8 from Auger spectroscopy data. Simultaneously, other metallic impurities were not increased substantially as a result of gettering. Additional effects observed during this study include a change in the accelerated deuterium species concentrations, loss of gettering activity and arc operation, and a change in arc performance from arc chamber gas absorption during operation

Pay dispersion, culture and bank performance

This chapter examines the impact of executive pay dispersion on firm performance and valuation in a global sample of banks. Controlling for cultural differences across countries, we test whether the equity fairness theory (favoring smaller pay dispersion) or tournament theory (arguing for greater pay dispersion) is a better description of the relationship between pay dispersion and performance. We find that the equity fairness theory prevails in most sub-groups of our sample, with the exception of Common Law developed country banks. We also find for our sample banks in Developed Countries that Individualism is positively associated with market valuation, while Uncertainty Avoidance has a negative effect