An automatic MRI quality control procedure: Multisite reports for slice thickness and geometric accuracy

In this work, we report multi-scanner quality control monitoring using a standard and automated protocol. This magnetic resonance imaging quality control protocol, based on the American College of Radiology procedures, includes weekly scans of a dedicated phantom followed by specific measurements. The processing step commonly involves manually-performed operations which can be tedious and time-consuming hence motivating their automation. QC data were collected in four sites; data from one of them served for the validation of the automatic analysis tool. Designed as a package of MATLAB^® functions, this tool was successfully validated using Student's t-test and the correlation between automatic measurements and the manual ones. Besides, the multisite QC study enabled to compare the performances of these four MR facilities. In order to avoid misinterpretation or errors in multicenter clinical studies, such approach can be recommended as a preliminary step for including a site in the studies.     

Assessing incomplete deprotection of microarray oligonucleotides in situ

En masse analysis of gene structure and function by array technologies will have a lasting and profound effect on biology and medicine. This impact can be compromised by low quality of probes within arrays, which we show can be caused by incomplete removal of chemical protecting groups. To solve this quality control problem, we present a sensitive, specific and facile method to detect these groups in situ on arrays using monoclonal antibodies and existing instrumentation. Screening of microarrays with these monoclonal antibodies should guide the consideration given to data derived from these and should enhance the accuracy of the results obtained.     

MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers

Major histocompatibility complex (MHC) class I chain-related gene B (MICB) encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8⁺ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE) on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI), whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024) present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations.     

Long-term changes in lowland calcareous grassland plots using <Emphasis Type="Italic">Tephroseris integrifolia</Emphasis> subsp. <Emphasis Type="Italic">integrifolia</Emphasis> as an indicator species

We investigated the changes to calcareous grassland plots within protected sites, and whether Tephroseris integrifolia subsp. integrifolia can act as a useful indicator species for re-visitation studies within vegetation predicted to remain relatively stable. Twenty-two plots located across lowland England and all formerly containing T. integrifolia were re-surveyed following the methodology used in the original survey undertaken in the 1960s. Pseudo-turnover and between-observer bias were minimised by sampling replicate quadrats at each fixed plot using a single surveyor and at a similar time of year as the original survey. Qualitative details concerning grazing management were obtained for all sites. In contrast to other long-term re-visitation studies, all our study plots were intact and retained diverse, herb-rich vegetation, demonstrating the value of site protection. However, there were clear shifts in vegetation composition, most notably where T. integrifolia was absent, as shown by an increase in Ellenberg fertility and moisture signifying nutrient enrichment, and a decrease in the cover of low-growing, light-demanding specialists, with a change likely to be associated predominantly with grazing management. Whereas in the mid-20th century the greatest threat to calcareous grassland was habitat loss, undergrazing or temporary neglect now appears to pose the principal threat. Distinctive species such as T. integrifolia with marked sensitivity to habitat change provide a potentially useful tool for rapid assessment and monitoring of site quality. Focusing monitoring on such species allows non-expert observers to recognise the early stages of habitat degradation, providing, in effect, a “health check” on individual sites and groups of sites.     

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation

Background

High-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generation sequencing (NGS) technologies. We investigate the Illumina GoldenGate chemistry using custom designed VeraCode and sentrix array matrix (SAM) assays for each of these applications, respectively. We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors.

Findings

We illustrate the dramatic effect of outliers in genotype calling and data interpretation, as well as suggest simple means to avoid genotyping errors. Furthermore we present this platform as a successful method for two-cluster rare or non-autosomal variant calling. The success of high-throughput technologies to accurately call rare variants will become an essential feature for future association studies. Finally, we highlight additional advantages of the Illumina GoldenGate chemistry in generating unusually segregated cluster plots that identify potential NGS generated sequencing error resulting from minimal coverage.

Conclusions

We demonstrate the importance of visually inspecting genotype cluster plots generated by the Illumina software and issue warnings regarding commonly accepted quality control parameters. In addition to suggesting applications to minimise data exclusion, we propose that the Illumina cluster plots may be helpful in identifying potential in-put sequence errors, particularly important for studies to validate NGS generated variation.

     

Timing of white-tailed deer browsing affects wetland plant communities

White-tailed deer (Odocoileus virginianus Zimm.) have the potential to alter plant community composition and successional trajectory by browsing differentially on forb, graminoid, and woody species. The objective of this study was to determine if seasonal elimination of deer browsing changed wetland plant community composition and structure. We established 66 deer exclosure plots in two wetland vegetation communities in Canaan Valley, West Virginia, USA. Plots were established in April 2005 and monitoring was conducted in June and October, 2005–2007 to obtain data on both early and late species. Composition differed between control and treatment plots in Solidago spp.–Rubus hispidus L. communities in late-protected plots (enclosed July–October) when data were gathered in October. Community composition also varied in early-protected plots (enclosed April–July) when data were gathered in June. Forb cover increased in treatment plots in Solidago spp.–Rubus hispidus communities. Composition differed in Populus tremuloides Michx. communities in late-protected and continuously protected plots. There was no increase in cover by any wetland indicator status categories after 2 years of protection. Timing of browse played an influential role in the effect that white-tailed deer have on wetland plant communities. Our results suggest that reducing browsing pressure seasonally can increase forb species cover.     

The prevalence of soil transmitted helminth infections in minority indigenous populations of South-East Asia and the Western Pacific Region: A systematic review and meta-analysis

IntroductionSoil transmitted helminth (STH) infections cause one of the most prevalent diseases in man. STHs disproportionately impact socio-economically disadvantaged communities including minority indigenous populations. This systematic review aimed to quantify the prevalence of STH infection within minority indigenous populations of the South-East Asia and Western Pacific Regions.MethodsThe systematic review was conducted in accordance with The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines following a published protocol. A random effects meta-analysis was used to estimate the pooled prevalence of STH infection, and meta-regression analysis was used to quantify associations with study characteristics. Where comparative data were available, sub-group analysis was conducted to evaluate the risk of STH infection in minority indigenous people relative to other population groups. The heterogeneity between studies was evaluated visually using Forest plots and was assessed quantitatively by the index of heterogeneity (I²) and Cochran Q-statistics.ResultsFrom 1,366 unique studies that were identified, 81 were included in the final analysis. The pooled prevalence of infection within minority indigenous populations was 61.4% (95% CI 50.8, 71.4) for overall STH infection; 32.3% (95% CI 25.7, 39.3) for Ascaris.lumbricoides; 43.6% (95% CI 32.6, 54.8) for Trichuris.trichiura; 19.9% (95% CI 15.7, 24.5) for hookworm and 6.3% (95% CI 3.2, 10.2) for Strongyloides.stercoralis. A significant increase in T. trichiura prevalence was observed over time. The stratified analysis showed that the prevalence of infection for STH overall and for each STH species were not significantly different in minority indigenous participants compared to other populations groups.ConclusionThe prevalence of STH infection is high within minority indigenous populations across countries at very different levels of socio-economic development. The increasing prevalence of T. trichiura calls for the implementation of more effective therapies and control strategies.     

cis-Jasmone indirect action on egg parasitoids (Hymenoptera: Scelionidae) and its application in biological control of soybean stink bugs (Hemiptera: Pentatomidae)

In many plants, the secondary metabolite cis-jasmone activates the metabolic pathway that produces volatile organic compounds attractive to natural enemies and, sometimes, repellent to herbivores. Previous studies indicate that the feeding damage caused by the herbivore Euschistus heros or the exogenous application of cis-jasmone in soybean plants induces the release of herbivore-induced plant volatiles (HIPVs) with a similar chemical profile and these compounds can attract the stink bug egg parasitoid Telenomus podisi (Scelionidae). Herein we tested in field conditions the effect of exogenous application of cis-jasmone in soybean plants on the parasitoid and stink bug community and on stink bug egg parasitism. In two areas, one within a soybean and another within a Crotalaria matrix, we randomly distributed 2 m² plots, with soybean plants induced (treatment, n = 5) or not induced by cis-jasmone (control, n = 5) in the field. We sampled the parasitoid community weekly with yellow sticky traps (n = 3/plot) and monitored parasitism with sentinel eggs of E. heros (n = 150/plot). We also monitored the population of stink bugs weekly, by sampling each plot with shake-cloth technique. The abundance of Scelionidae was highest overall and also in treated plots during the first four weeks in the area with a soybean matrix, but decreased thereafter. The richness of parasitoid families was similar between treatment and control plots in the area with a soybean matrix, but higher in control plots in the area with a Crotalaria matrix. Evenness was higher in control plots in the area with soybean matrix, whereas the reverse occurred in the area with a Crotalaria matrix. Results suggest that treatment with cis-jasmone effectively attracted and enhanced the population of scelionid parasitoids, but had no effect on the occurrence and intensity of parasitism and in the number of stink bugs.     

Do litter-feeding macroarthropods disrupt cascading effects of land use on microbial decomposer activity?

Plant traits are known to control litter decomposition rates through afterlife effects on litter quality. Land-use practices that modify plant traits, e.g. livestock grazing and soil fertilization, also have cascading effects on litter decomposition. However, almost all studies of these afterlife effects ignored the role of soil detritivores in the decomposition processes. We explored how the feeding activities of a macroarthropod modify microbial activity in leaf litter. Dead leaves from two grassland species, Bromopsis erecta and Potentilla verna, were collected in fertilized or unfertilized grazed plots and fertilized or unfertilized ungrazed plots. We determined how intraspecific variation in litter quality in response to sheep grazing and soil fertilization (i) influences the consumption and assimilation of leaf litter by the millipede Glomeris marginata, and (ii) affects the activity of microbial decomposers, assessed by substrate-induced respiration (SIR), in leaf litter before consumption and in faecal pellets and litter remains processed by Glomeris under all treatments. In the absence of millipedes, microbial activity was significantly higher in leaf litter from fertilized plots. Glomeris consumed larger amounts of leaf litter from fertilized grazed plots, owing to increased consumption of the otherwise poorly palatable Bromopsis, and produced larger amounts of faecal pellets when fed on this food. However, irrespective of the food consumed, SIR in faecal pellets was found to be similar in all treatments. Moreover, SIR in litter remains unconsumed at the end of the experiment was reduced to low and similar levels in all treatments. Overall, homogenization of microbial activity by Glomeris suppressed differences in SIR between leaf litter from fertilized and unfertilized plots, in both Bromopsis and Potentilla. Our results suggest that studies that assess afterlife effects of plant traits on decomposition using methods that exclude soil macrofauna may prove inadequate in ecosystems with abundant populations of detritivores.     

Effects of sowing native herbaceous species on the post-fire recovery in a heathland

Erica australis heathlands in León province (NW Spain) have high resilience to disturbances and their post-fire recovery is very fast. The risk of soil erosion is high in the first few months after fire. The aim of this study is to investigate the effects on post-fire succession of sowing grass (Agrostis capillaris and Festuca rubra) and legume (Lotus corniculatus) seeds in a heathland burned by a summer wildfire, and to determine the most suitable native herbaceous species combination for protecting the soil in the first few phases of recovery. Fifteen permanent 4 m² plots are established in the burned area; four treatments and a control (unsown) are applied, each with three replicates. Three similar unburned plots are also considered (unburned control). Total cover is significantly higher in the sown plots in relation to the control in the first few months after sowing, but there are no differences after 18 months. Lotus corniculatus appears only in the first year and has no effect on the total cover. F. rubra appears earlier than Agrostis capillaris, but decreases significantly in cover after 18 months. Shrub species have the highest cover in the control plots and the lowest in the Agrostis plots. The correspondence analysis shows that the trend for vegetation in all plots reaches similar species composition by the time of final sampling. The last sampling of sown plots shows greater similarity to the control plots than the sampling of these plots within the first year. The fast initial growth of F. rubra, together with its decrease and subsequent low cover from the second year, make it more preferable than Agrostis capillaris for purposes of soil protection. However, additional research, both species- and site-specific, is necessary, as different responses due to different post-fire conditions and pre-fire species composition can have important implications on community dynamics.     

Testing bespoke management of foraging habitat for European turtle doves Streptopelia turtur

Agri-environment schemes (AES) are increasingly being employed to mitigate biodiversity loss in agricultural environments. The European Turtle Dove Streptopelia turtur is an obligate granivorous bird in rapid decline within both the UK (−96% since 1970) and across continental Europe (−77% since 1980), despite widespread uptake of AES. Here, we assess the efficacy of a potentially new, sown agri-environment option designed to provide abundant, accessible seed for S. turtur during the breeding season. During summer 2011 we compared vegetation structure and seed provision on trial plots to control habitat types (existing agri-environment options thought to potentially provide S. turtur foraging habitat) to assess whether trial plots performed better for foraging S. turtur than control habitats. In September 2011 all trial plots were topped (cut) and half of a subset of trial plots were then scarified (60% of soil surface disturbed). Vegetation structure on topped, and topped and scarified trial plots was measured during summer 2012 to determine which management regime was most effective in maintaining suitable sward structure and seed provision into the second year. No control habitat type produced as much seed important in S. turtur diet as trial plots at any point during year one. Trial plots provided accessible vegetation structure early in the season with no difference in vegetation metrics between trial plots and previously published data on S. turtur foraging locations. However, to allow later access, management is required during mid-June to open up the sward through localized topping or scarification. Vegetation structure during year two was generally too dense to attract foraging S. turtur. However, scarifying trial plots during the September following sowing encouraged self-seeding of Fumaria. officinalis (a plant species historically forming a significant proportion of S. turtur diet during the breeding season) into the second year, with this species present in 16% of scarified trial plots compared to only 4% of topped trial plots during year two. Thus, autumn scarification, possibly followed by topping or scarification of part of the trial plots in June, is necessary for trial plots to provide more seed and access for S. turtur than existing agri-environment options during year two. We recommend modifications to our original seed mix in order to reduce vegetation density and improve vegetation structure. The study provides an example of the need to strike the right balance between food abundance and accessibility, through vegetation structure, when designing agri-environment scheme management options that provide food for birds.     

Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival

Background

Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed with three different experimental methods for the same set of neuroblastoma patients create opportunity to examine whether augmenting gene expression profiles with information on copy number variation can lead to improved predictions of patients survival. We propose methodology based on comprehensive cross-validation protocol, that includes feature selection within cross-validation loop and classification using machine learning. We also test dependence of results on the feature selection process using four different feature selection methods.

Results

The models utilising features selected based on information entropy are slightly, but significantly, better than those using features obtained with t-test. The synergy between data on genetic variation and gene expression is possible, but not confirmed. A slight, but statistically significant, increase of the predictive power of machine learning models has been observed for models built on combined data sets. It was found while using both out of bag estimate and in cross-validation performed on a single set of variables. However, the improvement was smaller and non-significant when models were built within full cross-validation procedure that included feature selection within cross-validation loop. Good correlation between performance of the models in the internal and external cross-validation was observed, confirming the robustness of the proposed protocol and results.

Conclusions

We have developed a protocol for building predictive machine learning models. The protocol can provide robust estimates of the model performance on unseen data. It is particularly well-suited for small data sets. We have applied this protocol to develop prognostic models for neuroblastoma, using data on copy number variation and gene expression. We have shown that combining these two sources of information may increase the quality of the models. Nevertheless, the increase is small and larger samples are required to reduce noise and bias arising due to overfitting.

Reviewers

This article was reviewed by Lan Hu, Tim Beissbarth and Dimitar Vassilev.

     

An improved method for monitoring parasitism and establishment of Oobius agrili (Hymenoptera: Encyrtidae), an egg parasitoid introduced for biological control of the emerald ash borer (Coleoptera: Buprestidae) in North America

Oobius agrili Zhang and Huang (Hymenoptera: Encyrtidae) is a solitary egg parasitoid that has been released in the United States since 2007 for biocontrol of the invasive emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). Field and laboratory trials with ash logs infested with EAB eggs were conducted in Michigan between 2009 and 2010 to improve methods for monitoring the establishment of O. agrili. Naturally occurring EAB eggs were collected in both parasitoid-release and control (non-parasitoid-release) plots to compare with the EAB egg-sentinel log (ESL) technique. In three parasitoid-release plots, >50% of ESLs had O. agrili-parasitized eggs ranging from 3.9% to 48.2% egg parasitism after one week of field exposure. No EAB eggs were attacked by O. agrili on the ESLs deployed in control plots. In the laboratory, 100% of ESLs exposed to O. agrili inside rearing jars for one week had parasitized-eggs (68.5% egg parasitism). Deployment of ESLs detected low levels of parasitism by O. agrili in all three ash stands where O. agrili was released in previous years. In contrast, collection of naturally occurring EAB eggs detected the parasitism in only one of these three parasitoid-release ash stands. No parasitism was detected in control ash stands with either method. These findings indicate that populations of O. agrili released in previous years had successfully overwintered and established in the released ash stands by 2010, but had not yet dispersed to the control stands.     

Impact of predatory carabids on below- and above-ground pests and yield in strawberry

The impact of adult carabid beetles on below- and above-ground pests and fruit yield was examined in the laboratory and a two-year strawberry field study. In the laboratory, adults of Carabus nemoralis Muller, Nebria brevicollis (F.), Pterostichus algidus LeConte, Pterostichus melanarius (Illiger), and Scaphinotus marginatus Fischer (Coleoptera: Carabidae) consumed black vine weevil, Otiorhynchus sulcatus (F.) (Coleoptera: Curculionidae) eggs, larvae and/or pupae placed on the surface. The same five carabid species showed no impact or low removal rates of O. sulcatus larvae that had burrowed into the root of potted strawberry plants. In an assay with only P. melanarius, adults consumed O. sulcatus larvae placed on the soil surface more frequently than larvae buried 1.3 or 5?cm below. In a field study, the density of adult carabids, predominantly P. melanarius, was manipulated with augmented, exclusion, and open control plots (2?×?2?m). Manipulating carabid density had no impact on the removal of sentinel O. sulcatus larvae and pupae that were buried belowground which is consistent with laboratory observations. Increasing carabid density within augmented plots led to greater removal of red clover seeds, Trifolium pratense L., placed on the soil surface in the first?year. Decreasing carabid density within exclusion plots resulted in fewer marketable fruits compared to control plots in both years. These results suggest that certain adult carabids may have limited impact belowground, and some beneficial impacts above-ground with pest control and crop protection.     

Utilization of harvester ant nest sites by Persian goitered gazelle in steppes of central Iran

Ants are among the most important elements in many ecosystems and known as famous ecosystem engineers. By changing physical and chemical properties of soil, ants may provide suitable habitats for other species. Based on previous observations, we hypothesized that Persian goitered gazelles (Gazella subgutturosa subgutturosa) exhibit a preference for utilizing sites close to seed harvester ant (Messor spp.) nests. We tested our hypothesis by (1) mapping the occurrence of harvester ant nests and aggregated gazelle pellet groups along 31 strip transects, (2) monitoring pellet group accumulation bimonthly at 56 pairs of permanent plots established on ant nests and at adjacent control sites for a complete year, and (3) comparing vegetation and soil parameters between ant nest sites used by gazelles and paired control plots without ant nests. Although the area of Messor spp. nest sites covered only about 0.29% of the sampled transects, 84% of the gazelle pellet group aggregation sites were positioned upon ant nests, suggesting that gazelles actively selected Messor spp. nest sites. Pair-wise comparisons between ant nest plots and paired control plots also confirmed higher use of ant nest sites by gazelles compared to sites without ant nests in all time periods. Percent soil organic matter, percent cover of gravel, and annual herb vegetation significantly differed between ant nest and paired control plots in all the vegetation communities. We suggest that the alterations brought about by harvester ants on soil and vegetation make these sites attractive to gazelles. Gazelle territoriality behaviour and use of ant nests as bedding sites may be the reasons for selection of ant nest sites by gazelles.