Characterization of complex networks: A survey of measurements

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics of processes executed on the network. The analysis, discrimination, and synthesis of complex networks therefore rely on the use of measurements capable of expressing the most relevant topological features. This article presents a survey of such measurements. It includes general considerations about complex network characterization, a brief review of the principal models, and the presentation of the main existing measurements. Important related issues covered in this work comprise the representation of the evolution of complex networks in terms of trajectories in several measurement spaces, the analysis of the correlations between some of the most traditional measurements, perturbation analysis, as well as the use of multivariate statistics for feature selection and network classification. Depending on the network and the analysis task one has in mind, a specific set of features may be chosen. It is hoped that the present survey will help the proper application and interpretation of measurements.Comment: A working manuscript with 78 pages, 32 figures. Suggestions of measurements for inclusion are welcomed by the author

I-TASSER server for protein 3D structure prediction

<p>Abstract</p> <p>Background</p> <p>Prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. The community-wide Critical Assessment of Structure Prediction (CASP) experiments have been designed to obtain an objective assessment of the state-of-the-art of the field, where I-TASSER was ranked as the best method in the server section of the recent 7th CASP experiment. Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions.</p> <p>Results</p> <p>An on-line version of I-TASSER is developed at the KU Center for Bioinformatics which has generated protein structure predictions for thousands of modeling requests from more than 35 countries. A scoring function (C-score) based on the relative clustering structural density and the consensus significance score of multiple threading templates is introduced to estimate the accuracy of the I-TASSER predictions. A large-scale benchmark test demonstrates a strong correlation between the C-score and the TM-score (a structural similarity measurement with values in [0, 1]) of the first models with a correlation coefficient of 0.91. Using a C-score cutoff > -1.5 for the models of correct topology, both false positive and false negative rates are below 0.1. Combining C-score and protein length, the accuracy of the I-TASSER models can be predicted with an average error of 0.08 for TM-score and 2 Å for RMSD.</p> <p>Conclusion</p> <p>The I-TASSER server has been developed to generate automated full-length 3D protein structural predictions where the benchmarked scoring system helps users to obtain quantitative assessments of the I-TASSER models. The output of the I-TASSER server for each query includes up to five full-length models, the confidence score, the estimated TM-score and RMSD, and the standard deviation of the estimations. The I-TASSER server is freely available to the academic community at <url>http://zhang.bioinformatics.ku.edu/I-TASSER</url>.</p

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, α-actinin can retain conformation, function, and strength. α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long rod domain. Using molecular dynamics and normal mode analysis, we suggest that the α-actinin rod domain has flexible terminal regions which can twist and extend under mechanical stress, yet has a highly rigid interior region stabilized by aromatic packing within each spectrin repeat, by electrostatic interactions between the spectrin repeats, and by strong salt bridges between its two anti-parallel monomers. By exploring the natural vibrations of the α-actinin rod domain and by conducting bending molecular dynamics simulations we also predict that bending of the rod domain is possible with minimal force. We introduce computational methods for analyzing the torsional strain of molecules using rotating constraints. Molecular dynamics extension of the α-actinin rod is also performed, demonstrating transduction of the unfolding forces across salt bridges to the associated monomer of the α-actinin rod domain

Mindfulness at Work: Positive Affect, Hope, and Optimism Mediate the Relationship Between Dispositional Mindfulness, Work Engagement, and Well-Being

Mindfulness has been described as a state of awareness characterized by refined attentional skills and a non-evaluative attitude toward internal and external events. Recently it has been suggested that higher levels of mindfulness may be beneficial in the workplace and first programs aiming to increase mindful awareness in occupational settings have been introduced. The current study underpins these developments with empirical evidence regarding the involved psychological processes, by investigating the relationship between dispositional mindfulness, work engagement and well-being in 299 adults in fulltime employment. As hypothesized, the results confirm that self-reported mindfulness predicts work engagement and general well-being. Furthermore, these relationships are mediated by positive job-related affect and psychological capital (hope, optimism, resiliency, and self-efficacy). Investigating mindfulness and psychological capital as multi-faceted concepts by means of structural equation modeling yielded a more precise picture. The ability to step back from automatic, habitual reactions to distress turned out to be the mindfulness facet most central for predicting work engagement and well-being. Furthermore, mindfulness exerts its positive effect on work engagement by increasing positive affect, hope, and optimism, which on their own and in combination enhance work engagement (full mediation). Well-being, on the other hand, is directly influenced by mindfulness, which exerts additional indirect influence via positive affect, hope and optimism (partial mediation). Although exploratory in nature, the results identify non-reactivity and non-judging as important mindfulness skills in the workplace

Teachers and Mindful Colouring to Tackle Burnout and Increase Mindfulness, Resiliency and Wellbeing

The number of teachers leaving the profession continues to increase at a worrying rate. Factors contributing to this include burnout, heightened levels of stress, anxiety and depression. The current study tested whether the use of mindful colouring would translate to improvements in wellbeing. Teachers from the UK (n = 35) were randomly assigned to a colouring mindfulness-based intervention or waitlist group. Participants completed four scales (burnout, wellbeing, resilience and mindfulness) and participated in a 5-day intervention of daily mindfulness colouring or continued their working week as usual. Results of repeated-measures ANOVA showed statistically significant lower levels of burnout, stress, depressive symptoms and anxiety in the mindfulness colouring condition, as well as increased levels of resilience and mindfulness. Findings from the current study support the use of mindfulness colouring to significantly enhance levels of wellbeing in teachers. The study also presents an inexpensive, highly accessible and effective self-help tool for this targeted non-clinical population