The dynamic evolutionary history of genome size in North American woodland salamanders

© 2017 Published by NRC Research Press. The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders

Bayesian stochastic blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.Comment: 44 pages, 16 figures. Code is freely available as part of graph-tool at https://graph-tool.skewed.de . See also the HOWTO at https://graph-tool.skewed.de/static/doc/demos/inference/inference.htm

Physiotherapy rehabilitation for osteoporotic vertebral fracture (PROVE) : study protocol for a randomised controlled trial

Background: Osteoporosis and vertebral fracture can have a considerable impact on an individual’s quality of life. There is increasing evidence that physiotherapy including manual techniques and exercise interventions may have an important treatment role. This pragmatic randomised controlled trial will investigate the clinical and cost-effectiveness of two different physiotherapy approaches for people with osteoporosis and vertebral fracture, in comparison to usual care. Methods/Design: Six hundred people with osteoporosis and a clinically diagnosed vertebral fracture will be recruited and randomly allocated to one of three management strategies, usual care (control - A), an exercise-based physiotherapy intervention (B) or a manual therapy-based physiotherapy intervention (C). Those in the usual care arm will receive a single session of education and advice, those in the active treatment arms (B + C) will be offered seven individual physiotherapy sessions over 12 weeks. The trial is designed as a prospective, adaptive single-blinded randomised controlled trial. An interim analysis will be completed and if one intervention is clearly superior the trial will be adapted at this point to continue with just one intervention and the control. The primary outcomes are quality of life measured by the disease specific QUALLEFO 41 and the Timed Loaded Standing test measured at 1 year. Discussion: There are a variety of different physiotherapy packages used to treat patients with osteoporotic vertebral fracture. At present, the indication for each different therapy is not well defined, and the effectiveness of different modalities is unknown

Empirically-Driven Multiwavelength K-corrections At Low Redshift

K-corrections, conversions between flux in observed bands to flux in rest-frame bands, are critical for comparing galaxies at various redshifts. These corrections often rely on fits to empirical or theoretical spectral energy distribution (SED) templates of galaxies. However, the templates limit reliable K-corrections to regimes where SED models are robust. For instance, the templates are not well-constrained in some bands (e.g., WISE W4), which results in ill-determined K-corrections for these bands. We address this shortcoming by developing an empirically-driven approach to K-corrections as a means to mitigate dependence on SED templates. We perform a polynomial fit for the K-correction as a function of a galaxy's rest-frame color determined in well-constrained bands (e.g., rest-frame (g-r)) and redshift, exploiting the fact that galaxy SEDs can be described as a one parameter family at low redshift (0.01 < z < 0.09). For bands well-constrained by SED templates, our empirically-driven K-corrections are comparable to the SED fitting method of Kcorrect and SED template fitting employed in the GSWLC-M2 catalogue (the updated medium-deep GALEX-SDSS-WISE Legacy Catalogue). However, our method dramatically outperforms the available SED fitting K-corrections for WISE W4. Our method also mitigates incorrect template assumptions and enforces the K-correction to be 0 at z = 0. Our K-corrected photometry and code are publicly available.Comment: 15 pages, 9 figures, submitted to MNRA

Local political leadership and the modernisation of local government

Political leadership has been a key element of central government’s attempts to ‘modernise’ local government over the past decade, within a discourse that emphasised ‘strong’ and ‘visible’ leadership and the role of leaders and leadership in driving change within local authorities. In the context of such an approach, and also taking account of academic discourse, this article draws upon interviews with nearly thirty individuals in leadership positions in local authorities in England, Scotland and Wales to assess their experiences of leadership and their views of some aspects of the role and work of councils. It suggests that whilst there is broad convergence between the aspirations of government and the narratives that emerge from these leaders on some aspects of local political leadership, there are also differences, perhaps most notably over the relationship between changes to decision making structures and the loci of political power

Stochastic oscillations of adaptive networks: application to epidemic modelling

Adaptive-network models are typically studied using deterministic differential equations which approximately describe their dynamics. In simulations, however, the discrete nature of the network gives rise to intrinsic noise which can radically alter the system's behaviour. In this article we develop a method to predict the effects of stochasticity in adaptive networks by making use of a pair-based proxy model. The technique is developed in the context of an epidemiological model of a disease spreading over an adaptive network of infectious contact. Our analysis reveals that in this model the structure of the network exhibits stochastic oscillations in response to fluctuations in the disease dynamic.Comment: 11 pages, 4 figure

Probing DNA conformational changes with high temporal resolution by Tethered Particle Motion

The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150~nm). Notably we demonstrate that, for a particle of radius 20~nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20~ms.Comment: Improved version, to appear in Physical Biology. 10 pages + 10 pages of supporting materia

The why, when, and how of computing in biology classrooms [version 1; peer review: 2 approved]

Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. Additionally, we review the literature on teaching practices to support the development of these skills. We pay special attention to meeting the needs of diverse learners, and consider how different ways of delivering course content can be leveraged to provide a more inclusive classroom experience. Our goal is to enable biologists to teach computational skills and use computing in the classroom successfully