P-value based visualization of codon usage data

Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the well-known chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases

Semi-automated quantification of left ventricular volumes and ejection fraction by real-time three-dimensional echocardiography

<p>Abstract</p> <p>Background</p> <p>Recent studies have shown that real-time three-dimensional (3D) echocardiography (RT3DE) gives more accurate and reproducible left ventricular (LV) volume and ejection fraction (EF) measurements than traditional two-dimensional methods. A new semi-automated tool (4DLVQ) for volume measurements in RT3DE has been developed. We sought to evaluate the accuracy and repeatability of this method compared to a 3D echo standard.</p> <p>Methods</p> <p>LV end-diastolic volumes (EDV), end-systolic volumes (ESV), and EF measured using 4DLVQ were compared with a commercially available semi-automated analysis tool (TomTec 4D LV-Analysis ver. 2.2) in 35 patients. Repeated measurements were performed to investigate inter- and intra-observer variability.</p> <p>Results</p> <p>Average analysis time of the new tool was 141s, significantly shorter than 261s using TomTec (<it>p </it>< 0.001). Bland Altman analysis revealed high agreement of measured EDV, ESV, and EF compared to TomTec (<it>p </it>= <it>NS</it>), with bias and 95% limits of agreement of 2.1 ± 21 ml, -0.88 ± 17 ml, and 1.6 ± 11% for EDV, ESV, and EF respectively. Intra-observer variability of 4DLVQ vs. TomTec was 7.5 ± 6.2 ml vs. 7.7 ± 7.3 ml for EDV, 5.5 ± 5.6 ml vs. 5.0 ± 5.9 ml for ESV, and 3.0 ± 2.7% vs. 2.1 ± 2.0% for EF (<it>p </it>= <it>NS</it>). The inter-observer variability of 4DLVQ vs. TomTec was 9.0 ± 5.9 ml vs. 17 ± 6.3 ml for EDV (<it>p </it>< 0.05), 5.0 ± 3.6 ml vs. 12 ± 7.7 ml for ESV (<it>p </it>< 0.05), and 2.7 ± 2.8% vs. 3.0 ± 2.1% for EF (<it>p </it>= <it>NS</it>).</p> <p>Conclusion</p> <p>In conclusion, the new analysis tool gives rapid and reproducible measurements of LV volumes and EF, with good agreement compared to another RT3DE volume quantification tool.</p

What are scoping reviews? Providing a formal definition of scoping reviews as a type of evidence synthesis.

Evidence synthesis encompasses a broad range of review types and scoping reviews are an increasingly popular approach to synthesizing evidence in a number of fields. They sit alongside other evidence synthesis methodologies such as systematic reviews, qualitative evidence synthesis, realist synthesis and many more. Until now, scoping reviews have been variously defined in the literature. In this article, we provide the following formal definition for scoping reviews: Scoping reviews are a type of evidence synthesis that aims to systematically identify and map the breadth of evidence available on a particular topic, field, concept, or issue, often irrespective of source (i.e. primary research, reviews, non-empirical evidence) within or across particular contexts. Scoping reviews can clarify key concepts/definitions in the literature and identify key characteristics or factors related to a concept, including those related to methodological research

The role of earthworm communities in soil mineral weathering in a field experiment

MINERALS are an important component of the soil environment (Dixon et al., 1977). They provide a structural framework which supports plants and contribute to the physical heterogeneity of soil. Minerals also contribute to the fertility of soils. Primary minerals are a source of essential plant nutrients (Harley and Gilkes, 2000). Clay minerals impact on the water-holding capacity of soils, affect the cation exchange capacity of soils (Brown, 1977) and are able to sequester nutrients and contaminants within the soil (Dubbin, 2001). Mineral weathering is an important process in soils and releases nutrients from the mineral structure into a form available for uptake by plants (Harley and Gilkes, 2000). Mineral weathering also increases the number of cation exchange sites, which increases the fertility of soils by improving nutrient retention. The weathering of clay minerals and the expansion of clay layers increases the water-holding capacity of soils (Brown, 1977). Mineral weathering also contributes to the pedological development of soils. Pedologically old soils are highly weathered and have a large proportion of clay minerals and a small proportion of primary minerals (Dubbin, 2001). Highly weathered soils, such as those found in the tropics, tend to be less fertile than less weathered soils (Dubbin, 2001). Earthworms are an important component of the soil ecosystem and have been described as ecosystem engineers because of the major role they play in modifying the soil ecosystem (Lavelle et al., 1997). They play a key role in modifying the physical structure of soils by creating aggregates (Haynes and Fraser, 1998), creating pores which increases infiltration and drainage (Lamande et al., 2003) and contributing to the development of soil horizons by the transport of material and incorporation of organic matter (Marhan and Scheu, 2006). Earthworms are also one of the key drivers of decomposition, particularly in temperate soil ecosystems by comminuting organic matter and incorporating it into the soil (McInerney and Bolger, 2000). Mineral weathering is a biogeochemical process in which organisms are intimately involved. Previous studies have shown that earthworms are capable of accelerating the weathering of soil minerals (Suzuki et al., 2003; Needham et al., 2004; Carpenter et al., 2007). However, this important interaction between two key components of the soil environment has not previously been studied in a field situation. The aim of this study was to evaluate the role of an earthworm community in the weathering of a primary mineral addition to a field soil

Adaptive-Focus Statistical Shape Model for Segmentation of 3D MR Structures

. This paper presents a deformable model for automatically segmenting objects from volumetric MR images and obtaining point correspondences, using geometric and statistical information in a hierarchical scheme. Geometric information is embedded into the model via an affine-invariant attribute vector, which characterizes the geometric structure around each model point from a local to a global level. Accordingly, the model deforms seeking boundary points with similar attribute vectors. This is in contrast to most deformable surface models, which adapt to nearby edges without considering the geometric structure. The proposed model is adaptive in that it initially focuses on the most reliable structures of interest, and subsequently switches focus to other structures as those become closer to their respective targets and therefore more reliable. The proposed techniques have been used to segment boundaries of the ventricles, the caudate nucleus, and the lenticular nucleus from v..