A simulation study comparing supertree and combined analysis methods using SMIDGen

<p>Abstract</p> <p>Background</p> <p>Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.</p> <p>Results</p> <p>In this paper, we describe an extensive simulation study we performed comparing two supertree methods, MRP and weighted MRP, to combined analysis methods on large model trees. A key contribution of this study is our novel simulation methodology (Super-Method Input Data Generator, or <it>SMIDGen</it>) that better reflects biological processes and the practices of systematists than earlier simulations. We show that combined analysis based upon maximum likelihood outperforms MRP and weighted MRP, giving especially big improvements when the largest subtree does not contain most of the taxa.</p> <p>Conclusions</p> <p>This study demonstrates that MRP and weighted MRP produce distinctly less accurate trees than combined analyses for a given base method (maximum parsimony or maximum likelihood). Since there are situations in which combined analyses are not feasible, there is a clear need for better supertree methods. The source tree and combined datasets used in this study can be used to test other supertree and combined analysis methods.</p

Sexual dimorphism in cancer.

The incidence of many types of cancer arising in organs with non-reproductive functions is significantly higher in male populations than in female populations, with associated differences in survival. Occupational and/or behavioural factors are well-known underlying determinants. However, cellular and molecular differences between the two sexes are also likely to be important. In this Opinion article, we focus on the complex interplay that sex hormones and sex chromosomes can have in intrinsic control of cancer-initiating cell populations, the tumour microenvironment and systemic determinants of cancer development, such as the immune system and metabolism. A better appreciation of these differences between the two sexes could be of substantial value for cancer prevention as well as treatment

Impact of inactivity and exercise on the vasculature in humans

The effects of inactivity and exercise training on established and novel cardiovascular risk factors are relatively modest and do not account for the impact of inactivity and exercise on vascular risk. We examine evidence that inactivity and exercise have direct effects on both vasculature function and structure in humans. Physical deconditioning is associated with enhanced vasoconstrictor tone and has profound and rapid effects on arterial remodelling in both large and smaller arteries. Evidence for an effect of deconditioning on vasodilator function is less consistent. Studies of the impact of exercise training suggest that both functional and structural remodelling adaptations occur and that the magnitude and time-course of these changes depends upon training duration and intensity and the vessel beds involved. Inactivity and exercise have direct “vascular deconditioning and conditioning” effects which likely modify cardiovascular risk

Quantifying the impacts of defaunation on natural forest regeneration in a global meta-analysis

Intact forests provide diverse and irreplaceable ecosystem services that are critical to human well-being, such as carbon storage to mitigate climate change. However, the ecosystem functions that underpin these services are highly dependent on the woody vegetation-animal interactions occurring within forests. While vertebrate defaunation is of growing policy concern, the effects of vertebrate loss on natural forest regeneration have yet to be quantified globally. Here we conduct a meta-analysis to assess the direction and magnitude of defaunation impacts on forests. We demonstrate that real-world defaunation caused by hunting and habitat fragmentation leads to reduced forest regeneration, although manipulation experiments provide contrasting findings. The extirpation of primates and birds cause the greatest declines in forest regeneration, emphasising their key role in maintaining carbon stores, and the need for national and international climate change and conservation strategies to protect forests from defaunation fronts as well as deforestation fronts

Bias induced diamond nucleation studies on refractory metal substrates

The carbide forming nature of the substrate appears to be an important property when performing bias-enhanced nucleation (BEN); therefore, various refractory metals were studied since they are known carbide formers. Nucleation densities approaching 1×1010/cm2 were observed on both hafnium and titanium. The nucleation density on tantalum, niobium, and tungsten was enhanced to a lesser extent in descending order of influence, respectively. An induction time prior to the onset of significant diamond nucleation was observed on the refractory metals as well as on silicon and may be reliant upon the formation of a critical carbide thickness. Shorter induction times were observed for silicon which may be explained since this material forms a carbide of typically only several nanometers in thickness as opposed to the refractory metals which may form carbides on the order of several microns in thickness. Also, a strong correlation was observed between the carbide heat of formation and the nucleation densities at 60 min of BEN. These findings verify the relevance of a carbide formation to diamond nucleation via BEN and also provides a clue as to the mechanism(s) by which diamond is nucleating. © 1995 American Institute of Physics

Graphenated carbon nanotubes for enhanced electrochemical double layer capacitor performance

This letter reports on nucleation and growth of graphene foliates protruding from the sidewalls of aligned carbon nanotubes (CNTs) and their impact on the electrochemical double-layer capacitance. Arrays of CNTs were grown for different time intervals, resulting in an increasing density of graphene foliates with deposition time. The samples were characterized using electrochemical impedance spectroscopy, scanning electron microscopy, and transmission electron microscopy. Both low and high frequency capacitance increased with increasing foliate density. A microstructural classification is proposed to explain the role of graphene edges, three-dimensional organization, and other features of hybrid carbon systems on their electrochemical properties. © 2011 American Institute of Physics