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Concept: Functional analysis

171

SUMMARY: Pathview is a novel tool set for pathway based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway, and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. AVAILABILITY: The package is freely available under the GPLv3 licence through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. CONTACT: luo_weijun@yahoo.com.

Concepts: Mathematics, Integral, Vector space, Derivative, Functional analysis

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There is increasing public and scientific concern regarding the long-term behavioural effects of video game use in children, but currently little consensus as to the nature of any such relationships. We investigated the relationship between video game use in children, degree of violence in games, and measures of depression and a 6-level banded measure of conduct disorder. Data from the Avon Longitudinal Study of Parents and Children were used. A 3-level measure of game use at age 8/9 years was developed, taking into account degree of violence based on game genre. Associations with conduct disorder and depression, measured at age 15, were investigated using ordinal logistic regression, adjusted for a number of potential confounders. Shoot-em-up games were associated with conduct disorder bands, and with a binary measure of conduct disorder, although the strength of evidence for these associations was weak. A sensitivity analysis comparing those who play competitive games to those who play shoot-em-ups found weak evidence supporting the hypothesis that it is violence rather than competitiveness that is associated with conduct disorder. However this analysis was underpowered, and we cannot rule out the possibility that increasing levels of competition in games may be just as likely to account for the observed associations as violent content. Overall game exposure as indicated by number of games in a household was not related to conduct disorder, nor was any association found between shoot-em-up video game use and depression.

Concepts: Scientific method, Psychology, Logistic regression, Measurement, Sociology, Functional analysis, Game, Video game genres

51

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face.

Concepts: Function, Jellyfish, Periodic function, Order theory, Functional analysis, Evidence, Scientific evidence, Anecdotal evidence

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In the present study, we examined the ability of the recombinant spidroin to serve as a substrate for the cardiac tissue engineering. For this purpose, isolated neonatal rat cardiomyocytes were seeded on the electrospun spidroin fiber matrices and cultured to form the confluent cardiac monolayers. Besides the adhesion assay and immunostaining analysis, we tested the ability of the cultured cardiomyocytes to form a functional cardiac syncytium by studying excitation propagation in the cultured tissue with the aid of optical mapping. It was demonstrated that recombinant spidroin fiber meshes are directly suitable for the adherence and growth of the cardiomyocytes without additional coating with the attachment factors, such as fibronectin.

Concepts: Present, Blood, Extracellular matrix, Cardiac muscle, Engineering, Hilbert space, Functional analysis, Calculus of variations

32

We aimed to estimate the prevalence of overweight and obesity, represented by extra body weight and abdominal circumference, among older Indians; and to characterise the social pattern of obesity and measure the magnitude of hypertension attributable to it.

Concepts: Epidemiology, Cancer, Nutrition, Obesity, Overweight, Adipose tissue, Body shape, Functional analysis

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Healthy aging has been associated with decreased specialization in brain function. This characterization has focused largely on describing age-accompanied differences in specialization at the level of neurons and brain areas. We expand this work to describe systems-level differences in specialization in a healthy adult lifespan sample (n = 210; 20-89 y). A graph-theoretic framework is used to guide analysis of functional MRI resting-state data and describe systems-level differences in connectivity of individual brain networks. Young adults' brain systems exhibit a balance of within- and between-system correlations that is characteristic of segregated and specialized organization. Increasing age is accompanied by decreasing segregation of brain systems. Compared with systems involved in the processing of sensory input and motor output, systems mediating “associative” operations exhibit a distinct pattern of reductions in segregation across the adult lifespan. Of particular importance, the magnitude of association system segregation is predictive of long-term memory function, independent of an individual’s age.

Concepts: Brain, Monotonic function, Function, Convex function, Magnetic resonance imaging, Systems theory, C, Functional analysis

27

Kernel machines traditionally arise from an elegant formulation based on measuring the smoothness of the admissible solutions by the norm in the reproducing kernel Hilbert space (RKHS) generated by the chosen kernel. It was pointed out that they can be formulated in a related functional framework, in which the Green’s function of suitable differential operators is thought of as a kernel. In this letter, our own picture of this intriguing connection is given by emphasizing some relevant distinctions between these different ways of measuring the smoothness of admissible solutions. In particular, we show that for some kernels, there is no associated differential operator. The crucial relevance of boundary conditions is especially emphasized, which is in fact the truly distinguishing feature of the approach based on differential operators. We provide a general solution to the problem of learning from data and boundary conditions and illustrate the significant role played by boundary conditions with examples. It turns out that the degree of freedom that arises in the traditional formulation of kernel machines is indeed a limitation, which is partly overcome when incorporating the boundary conditions. This likely holds true in many real-world applications in which there is prior knowledge about the expected behavior of classifiers and regressors on the boundary.

Concepts: Hilbert space, Vector space, Derivative, Operator, Functional analysis, Kernel trick, Reproducing kernel Hilbert space, Differential operator

27

Results of high-energy X-ray diffraction experiments coupled to atomic pair distribution function analysis of disordered low-Z materials are presented. Several scientifically and technologically important classes of disordered low-Z materials such as small and large organic molecules, graphitic powders, polymers and liquids are intentionally explored to certify the technique’s performance. Results clearly show that disordered low-Z materials can be well characterized in terms of material’s phase identity, relative abundance in mixtures and atomic-scale structure. The demonstrated efficiency of the technique provides the scientific community with much needed confidence to apply it more often than now.

Concepts: Scientific method, Chemistry, Science, Chemical substance, Calculus, X-ray crystallography, Functional analysis, Distribution function

26

The purpose of this study was to examine proverb interpretation performance and functional independence in older adults. From the limited literature on proverb interpretation in aging and its conceptualization as an executive function, it was hypothesized that proverb interpretation would be related to functional independence similar to other executive functions. Tests of proverb interpretation, additional executive functions, and functional ability were administered to nondemented older adults. Results showed that proverb interpretation accounted for a significant amount of unique variance of functional ability scores. This supports including a measure of proverb interpretation to the assessment of older adults.

Concepts: Probability theory, Lambda calculus, Working memory, Functional analysis, Executive functions, Stroop effect