Comparing the Cervista HPV HR Test and Hybrid Capture 2 Assay in a Dutch Screening Population: Improved Specificity of the Cervista HPV HR Test by Changing the Cut-Off

The diagnostic performance of the widely-used Cervista HPV HR test was compared to the Hybrid Capture 2 (HC2) test in a Dutch population-based cervical cancer screening program. In 900 scrapings of women with normal cytomorphology, specificity was 90% (95%CI: 87.84–91.87) for the Cervista HPV HR test and 96% (95%CI: 94.76–97.37) for the HC2 test with 93% agreement between both tests (κ = 0.5, p<0.001). The sensitivity for CIN2+ using 65 scrapings of women with histological-confirmed CIN2+ was 91% (95%CI: 80.97–96.51) for the Cervista HPV HR test and 92% (95%CI: 82.94–97.43) for the HC2 test with 95% agreement between both tests (κ = 0.7, p<0.001). Fifty-seven of 60 HC2 negative/Cervista positive cases tested HPV-negative with PCR-based HPV assays; of these cases 56% were defined as Cervista triple-positive with FOZ values in all 3 mixes higher than the second cut-off of 1.93 (as set by manufacturer). By setting this cut-off at 5.0, specificity improved significantly without affecting sensitivity. External validation of this new cut-off at 5.0 in triple-positive scrapings of women selected from the SHENCCASTII database revealed that 22/24 histological normal cases now tested HPV-negative in the Cervista HPV HR test, while CIN2+ lesions remained HPV-positive. The intra-laboratory reproducibility of the Cervista HPV HR test (n = 510) showed a concordance of 92% and 93% for cut-off 1.93 and 5.0 (κ = 0.83 and κ = 0.84, p<0.001) and inter-laboratory agreement of the Cervista HPV HR test was 90% and 93% for cut-off 1.93 and 5.0 (κ = 0.80 and κ = 0.85, p<0.001). In conclusion, the specificity of the Cervista HPV HR test could be improved significantly by increasing the second cut-off from 1.93 to 5.0, without affecting the sensitivity of the test in a population-based screening setting.     

Population Connectivity Shifts at High Frequency within an Open-Coast Marine Protected Area Network

A complete understanding of population connectivity via larval dispersal is of great value to the effective design and management of marine protected areas (MPA). However empirical estimates of larval dispersal distance, self-recruitment, and within season variability of population connectivity patterns and their influence on metapopulation structure remain rare. We used high-resolution otolith microchemistry data from the temperate reef fish Hypsypops rubicundus to explore biweekly, seasonal, and annual connectivity patterns in an open-coast MPA network. The three MPAs, spanning 46 km along the southern California coastline were connected by larval dispersal, but the magnitude and direction of connections reversed between 2008 and 2009. Self-recruitment, i.e. spawning, dispersal, and settlement to the same location, was observed at two locations, one of which is a MPA. Self-recruitment to this MPA ranged from 50–84%; within the entire 60 km study region, self-recruitment accounted for 45% of all individuals settling to study reefs. On biweekly time scales we observed directional variability in alongshore current data and larval dispersal trajectories; if viewed in isolation these data suggest the system behaves as a source-sink metapopulation. However aggregate biweekly data over two years reveal a reef network in which H. rubicundus behaves more like a well-mixed metapopulation. As one of the few empirical studies of population connectivity within a temperate open coast reef network, this work can inform the MPA design process, implementation of ecosystem based management plans, and facilitate conservation decisions.     

A Robust Post-Processing Workflow for Datasets with Motion Artifacts in Diffusion Kurtosis Imaging

Purpose

The aim of this study was to develop a robust post-processing workflow for motion-corrupted datasets in diffusion kurtosis imaging (DKI).

Materials and methods

The proposed workflow consisted of brain extraction, rigid registration, distortion correction, artifacts rejection, spatial smoothing and tensor estimation. Rigid registration was utilized to correct misalignments. Motion artifacts were rejected by using local Pearson correlation coefficient (LPCC). The performance of LPCC in characterizing relative differences between artifacts and artifact-free images was compared with that of the conventional correlation coefficient in 10 randomly selected DKI datasets. The influence of rejected artifacts with information of gradient directions and b values for the parameter estimation was investigated by using mean square error (MSE). The variance of noise was used as the criterion for MSEs. The clinical practicality of the proposed workflow was evaluated by the image quality and measurements in regions of interest on 36 DKI datasets, including 18 artifact-free (18 pediatric subjects) and 18 motion-corrupted datasets (15 pediatric subjects and 3 essential tremor patients).

Results

The relative difference between artifacts and artifact-free images calculated by LPCC was larger than that of the conventional correlation coefficient (p<0.05). It indicated that LPCC was more sensitive in detecting motion artifacts. MSEs of all derived parameters from the reserved data after the artifacts rejection were smaller than the variance of the noise. It suggested that influence of rejected artifacts was less than influence of noise on the precision of derived parameters. The proposed workflow improved the image quality and reduced the measurement biases significantly on motion-corrupted datasets (p<0.05).

Conclusion

The proposed post-processing workflow was reliable to improve the image quality and the measurement precision of the derived parameters on motion-corrupted DKI datasets. The workflow provided an effective post-processing method for clinical applications of DKI in subjects with involuntary movements.     

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation

Eukaryotic ribosome biogenesis involves ∼200 assembly factors, but how these contribute to ribosome maturation is poorly understood. Here, we identify a network of factors on the nascent 60S subunit that actively remodels preribosome structure. At its hub is Rsa4, a direct substrate of the force-generating ATPase Rea1. We show that Rsa4 is connected to the central protuberance by binding to Rpl5 and to ribosomal RNA (rRNA) helix 89 of the nascent peptidyl transferase center (PTC) through Nsa2. Importantly, Nsa2 binds to helix 89 before relocation of helix 89 to the PTC. Structure-based mutations of these factors reveal the functional importance of their interactions for ribosome assembly. Thus, Rsa4 is held tightly in the preribosome and can serve as a “distribution box,” transmitting remodeling energy from Rea1 into the developing ribosome. We suggest that a relay-like factor network coupled to a mechano-enzyme is strategically positioned to relocate rRNA elements during ribosome maturation.     

Long-term change in growth, mortality and regeneration of trees in Denny Wood, an old-growth wood-pasture in the New Forest (UK)

Long-term changes in stand composition and structure were recorded in Denny Wood (New Forest, UK) by means of a permanent transect covering 2 ha. Denny is an ancient, mixed deciduous wood-pasture dominated by beech (Fagus sylvatica), pedunculate oak (Quercus robur) and holly (Ilex aquifolium) whose canopy trees ranged in age from approximately 70 years to over 300 years when the study began in 1956. Individual trees, shrubs and saplings were mapped and measured at irregular intervals until 1996.

During the 40 years of observations, storms and drought disrupted the stand. Considerable volumes of dead wood accumulated, and canopy gaps extended to 30% of the transect area. Small trees and saplings were severely damaged by ponies and grey squirrels. Regeneration ceased after 1964, due principally to heavy grazing and browsing by deer and ponies. Despite the disturbances, most mortality was due to competitive exclusion within well-stocked parts of the stand.

Historical records from the 17th century onwards demonstrate a long-term change from oak dominance with groups of beech before 1800 to beech dominance in the late 20th century. The stand through which the transect now runs was enclosed in 1870, and this allowed beech to regenerate abundantly, but in the nearby unenclosed part of Denny Wood holly regenerated more abundantly than beech.

The patterns of growth, mortality and regeneration are compared with natural temperate deciduous woodland. The long-term relationship between beech and oak is likely to involve periodic oak regeneration after major disturbances, interspersed with steady increases in the proportion of beech. The implications for managing and monitoring the “Ancient and Ornamental Woods” of the New Forest are considered.     

On the correlation between allocation to defence and regrowth in plants

Because storage of resources to regrow after damage and investment in defence draw upon the same resource pool, it has been argued that they should show a negative correlation. We sketch a model for optimal allocation to defence and to storage for regrowth. In the model generalist herbivores exert a constant herbivore pressure against which the plant can defend itself. With discrete intervals, disturbance occurs by an external cause against which the plant cannot defend. This could be an abiotic disturbance or the outbreak of a specialist herbivore that is unaffected by the defence. If we compare genotypes or species, each adapted to its own habitat, then a positive correlation or no correlation between allocation to defence and to regrowth is to be expected. The parameter space in which plants should both defend and store resources for regrowth is limited. Especially under favourable growing conditions, plants should only allocate to growth. We discuss some experimental measures of the regrowth capacity of plants in the context of our model and argue that these should be used with caution.     

Review: Transport of tRNA out of the Nucleus—Direct Channeling to the Ribosome?

Although tRNA was the first substrate whose export from the nuclei of eukaryotic cells had been shown to be carrier-mediated and active, it has only been in the last 2 years that the first mechanistic details of this nucleocytoplasmic transport pathway have begun to emerge. A member of the importin/karyopherin β superfamily, Los1p in yeast and Xpo-t in vertebrates, has been shown to export tRNA in cooperation with the small GTPase Ran (Gsp1p) from the nucleus into the cytoplasm, where tRNA becomes available for translation. However, Los1p is not essential for viability in yeast cells, suggesting that alternative tRNA export pathways exist. Recent results show that aminoacylation and a translation factor are also required for efficient nuclear tRNA export. Thus, protein translation and nuclear export of tRNA appear to be coupled processes.     

Effects of Soil Texture on Belowground Carbon and Nutrient Storage in a Lowland Amazonian Forest Ecosystem

Soil texture plays a key role in belowground C storage in forest ecosystems and strongly influences nutrient availability and retention, particularly in highly weathered soils. We used field data and the Century ecosystem model to explore the role of soil texture in belowground C storage, nutrient pool sizes, and N fluxes in highly weathered soils in an Amazonian forest ecosystem. Our field results showed that sandy soils stored approximately 113 Mg C ha^-1 to a 1-m depth versus 101 Mg C ha^-1 in clay soils. Coarse root C represented a large and significant ecosystem C pool, amounting to 62% and 48% of the surface soil C pool on sands and clays, respectively, and 34% and 22% of the soil C pool on sands and clays to 1-m depth. The quantity of labile soil P, the soil C:N ratio, and live and dead fine root biomass in the 0–10-cm soil depth decreased along a gradient from sands to clays, whereas the opposite trend was observed for total P, mineral N, potential N mineralization, and denitrification enzyme activity. The Century model was able to predict the observed trends in surface soil C and N in loams and sands but underestimated C and N pools in the sands by approximately 45%. The model predicted that total belowground C (0–20 cm depth) in sands would be approximately half that of the clays, in contrast to the 89% we measured. This discrepancy is likely to be due to an underestimation of the role of belowground C allocation with low litter quality in sands, as well as an overestimation of the role of physical C protection by clays in this ecosystem. Changes in P and water availability had little effect on model outputs, whereas adding N greatly increased soil organic matter pools and productivity, illustrating the need for further integration of model structure and tropical forest biogeochemical cycling. Received 3 March 1999; accepted 27 August 1999.     

Surfactant aggregates (solloids) adsorbed on silica as stationary chromatographic phases: structures and properties

The structure and physical properties of solloids (surfactant aggregates adsorbed on surfaces) adsorbed on particles are of general interest. The relationship between solloid structure and properties of hexadecyltrimethylammonium bromide (HTAB), cetylpyridinium chloride (CPC) and cetylpyridinium salicylate (CPS) adsorbed on silica particles was studied by electron paramagnetic resonance (EPR) spectroscopy using the spin-probes peroxylaminedisulfonate (PADS) and 4-[N,N-dimethyl-N-(n-hexadecyl)ammonium]-2,2,6,6-tetramethylpiperidinyl-N-oxy bromide (HTAB*). Using HTAB* incorporated in HTAB, CPC and CPC solloids and comparing the results to those in micelles, it was determined that for silica around pH 4 the solloids are very similar in properties to the micelles. This is consistent with a linear solvation–energy relationship (LSER) analysis of solute equilibration data which indicates that at pH 5 HTAB solloids have similar properties to HTAB micelles. The PADS spin-probe appears to be more sensitive to changes in the properties of the double layer, and substantial differences were observed between HTAB, CPC and CPS and as a function of HTAB concentration for HTAB solloids on silica.