Inter‐ and intra‐observer variation in the reporting of cervical smears: specialist cytopathologists versus histopathologists

One hundred and ten cervical smears were circulated to five specialist consultant cytopathologists and five consultant histopathologists. Of these smears, 100 were randomized and re‐circulated. The cytopathologists reported endocervical cells and wart virus infection more frequently than the histopathologists, although neither group showed good inter‐observer agreement for either assessment. Apart from smear adequacy and the presence of endocervical cells, both groups showed good intra‐observer agreement in all the parameters measured. This suggests that overall individuals were applying their own personal criteria with consistency over time, although a previous study had shown considerable lack of inter‐observer agreement among the histopathologists on the grade of dyskaryosis and the management recommendation. The results indicate that specialist cytopathologists bring a different viewpoint to the reporting of cervical smears than histopathologists. They also show a lack of standardization in the reporting of smears despite the guidelines issued by the British Society for Clinical Cytology.     

Repeatability,reproducibility, and agreement of three computational methods to approximate the functional flexion-extension axis of the tibiofemoral joint using 3D bone models of the femur

Abstract

Background: Closely approximating the functional flexion-extension (FE) axis of the tibiofemoral joint in 3D models of the femur is important when computing joint motions which are physiologic. The objectives were to 1) develop methods to approximate the functional FE axis based on fitting circles, a tapered cylinder, and spheres to the posterior condyles, 2) determine the repeatability and reproducibility of each method, and 3) determine limits of agreement between pairs of axes.

Methods: For each method, the respective axis was determined in forty 3D bone models of the distal femur. Varus-valgus angles and internal-external axial angles were computed relative to standard planes.

Results: Repeatability and reproducibility were comparable for the tapered cylinder-based and sphere-based methods and better than that for the circle-based method. Limits of agreement were tightest when comparing the sphere-based and tapered cylinder-based axes. However, limits of agreement for the internal-external axial angle were wide at +3.6° to ?3.9° whereas limits of agreement were tighter at +1.4° to ?0.7° for the varus-valgus angle.

Conclusion: The tapered cylinder-based and sphere-based methods offer advantages of better repeatability and reproducibility over the circle-based method. However, the sphere-based and tapered cylinder-based axes are not interchangeable owing to wide limits of agreement for the internal-external axial angle. The tapered cylinder-based axis is preferred intuitively over the sphere-based axis because the spheres require fitting in both the sagittal and coronal planes whereas the tapered cylinder requires fitting in the sagittal plane only which is the plane of motion in flexion-extension.     

Fast egg collection method greatly improves randomness of egg sampling in Drosophila melanogaster

When obtaining samples for population genetic studies, it is essential that the sampling is random. For Drosophila, one of the crucial steps in sampling experimental flies is the collection of eggs. Here an egg collection method is presented, which randomizes the eggs in a water column and diminishes environmental variance. This method was compared with a traditional egg collection method where eggs are collected directly from the medium. Within each method the observed and expected standard deviations of egg-to-adult viability were compared, whereby the difference in the randomness of the samples between the two methods was assessed. The method presented here was superior to the traditional method. Only 14% of the samples had a standard deviation higher than expected, as compared with 58% in the traditional method. To reduce bias in the estimation of the variance and the mean of a trait and to obtain a representative collection of genotypes, the method presented here is strongly recommended when collecting eggs from Drosophila.     

Multi-scale comparisons of cliff vegetation in Colorado

We developed a nested vegetation sampling protocol to sample the plant diversity on south-facing cliffs and cliff bases in Jefferson County, Colorado. The multi-scale plots included three nested spatial scales, 1 m², 20 m², and 40 m². We compared plant species richness and species diversity among large cliffs, medium cliffs, small cliffs, and non-cliff sites using Hill's diversity numbers (N ₀, N ₁, and N ₂) for the 1-m² quadrats. Species richness (N ₀) was calculated for the 20-m² and 40-m² plots. Our results indicate that plant species diversity on the cliff faces did not increase with increasing cliff area. This pattern was consistent at all three sampling scales. A model selection was run to determine if plant species diversity values on the cliff faces were associated with cliff variables. None of the cliff variables measured were good predictors of diversity at the 1-m² scale. However, at the 20-m² scale, canyon differences and a positive relationship with increasing cliff surface roughness explained 70% of the variability in species richness. Although most plant species sampled on the cliff faces were also found in the base plots, 13 species were sampled only on the cliff faces. Additionally, dry south facing cliffs support a mix of xeric and mesic plants indicating that cliffs may provide unique microenvironments for plant establishment. This revised version was published online in August 2006 with corrections to the Cover Date.     

Considerations for ecological reconstruction of historic vegetation: Analysis of the spatial uncertainties in the California Vegetation Type Map dataset

Historical ecological data are valuable for reconstructing early environmental and vegetation community conditions and examining change to vegetation communities and disturbance regimes over decadal and longer temporal scales, but these data are not free from error. We examine the spatial uncertainties associated with 18,000 vegetation plots in the decades-old California Vegetation Type Mapping (VTM) dataset that has been digitized for use in modern ecological analysis. We examine the relationship between plot location error and basemap year, basemap scale, plot elevation, plot slope, and general plot habitat type. Bivariate plots and classification and regression tree analysis (CART) confirm that basemap scale and age are the strongest explanation of total error. Total error in spatial location for all plots ranged from 126.9 m to 462.3 m; plots drawn on 15-min (1:62,500-scale) basemaps had total error ranging from 126 m to 199.7 m, and plots drawn on coarser-scale basemaps (1:125,000-scale) had total errors ranging from 241 m to 461.2 m. Relocation of individual VTM plots is considerably easier for plots originally marked on 1:62,500-scale maps produced after 1904, and more difficult for plots originally marked on 1:125,000-scale maps produced before 1898. Biogeographical analyses that rely less on relocating individual plots, such as environmental niche modeling or multivariate analyses can alleviate some of these concerns, but all researchers using these kinds of data need to consider errors in spatial location of plots. The paper also discusses ways in which the differing spatial error might be reported and visualized by those using the dataset, and how the data might be used in modern environmental niche models.     

Higher level taxonomy and molecular phylogenetics of the Choanoflagellatea

The choanoflagellates (Choanoflagellatea) comprise a major group of nanoflagellates, which are ubiquitous in the aquatic environment. Recent molecular phylogenies have shown them to be the sister group to the Metazoa. However, the phylogeny of the choanoflagellates is still far from understood. We present here a 29 taxon, multigene phylogeny that robustly places the root of the choanoflagellates. One of the original nonloricate families, Codonosigidae is shown to be a polyphyletic assemblage nested within the Salpingoecidae. We elaborate on a revised taxonomy that divides Choanoflagellatea into two orders: Craspedida and Acanthoecida. Craspedida is composed of species that possess an organic cell coating and contains the single family Salpingoecidae. Members of the predominantly marine Acanthoecida produce a siliceous lorica in addition to an organic coat and are contained in two families--the Acanthoecidae and Stephanoecidae fam. n. Previous studies of choanoflagellates have been hindered by cases of taxon misidentification as well as the limited resolution of 18S small subunit (SSU) rDNA phylogenies. Unfortunately, cases of misidentification have been heavily repeated in the literature. In an attempt to avoid further confusion, we highlight known instances of misnamed taxa. We also examine the suitability of SSU rDNA sequences alone for choanoflagellate phylogenetics and recommend the use of protein-coding genes, such as hsp90 and tubA, whenever possible.