Intra- and interobserver assessments of intestinal wall thickness and segmentations from transverse sections of feline abdominal ultrasound images

Measurements of intestinal wall thicknesses from ultrasound imaging (US) are routinely used to support diagnoses of intestinal disorders in cats, however published studies describing observer agreement are currently lacking. The aim of this retrospective, observer agreement study was to quantify inter- and intraobserver repeatability and agreement in the measurement of intestinal wall layer thicknesses and the segmentation of transverse sections of small intestines in US images of 20 cats. Intestinal wall layer thickness measurements of the mucosa, submucosa, muscularis, serosa layer, and total thickness of these layers were performed on five cats with small cell epitheliotropic lymphoma, five with inflammatory bowel disease, and 10 with other conditions. Thickness measurements and the segmentation encompassing the serosa layer were obtained from five observers four times non-sequentially. The average standard deviation in thickness measurements (95% confidence interval) in the mucosa, submucosa, muscularis, serosa, and total thickness were 0.35 (0.07–0.95), 0.24 (0.07-0.52), 0.22 (0.06-0.49), 0.20 (0.05-0.49), and 0.57 (0.11-1.60) mm, respectively. The average intraclass correlation coefficients, which estimates the degree of consistency in thickness measurements and segmentation areas for each observer, ranged from 0.355 to 0.870 and 0.850 to 0.993, respectively. The interclass correlation coefficient, which estimates the degree of consistency when measuring a thickness or segmentation area over all observers ranged from 0.115 to 0.753, and 0.811 to 0.902, respectively. The overall average Dice Coefficient, which estimates the extent of overlap of the segmentations for all observers was 0.957 (0.933 to 0.972). Our results suggest segmentations of small intestines have a higher interobserver agreement than measurements of intestinal wall thicknesses.     

Evaluation of 'quick and dirty' DNA extraction methods for marker-assisted selection in rice (Oryza sativa L.)

Six simple methods for extracting DNA from rice seedlings were evaluated for marker‐assisted selection (MAS). The assessment of each method was based on PCR amplification of SSR markers, DNA yield and purity, time and cost. Based on these criteria, two methods were selected as being superior to other methods. The best two methods included the standard method developed at the International Rice Research Institute (IRRI), which utilizes a sodium dodecyl sulfate extraction buffer followed by chloroform/isoamyl alcohol extraction and a previously published method using sodium hydroxide and Tris. These two methods produced nearly identical PCR amplification results. The sodium hydroxide method is considerably simpler, quicker and cheaper than the standard IRRI method, and may be particularly useful for many applications of MAS or high‐resolution mapping. This method was also adapted into an effective high throughput method utilizing 96‐well plates emphasizing its versatility.     

Growth,symbiosis, productivity,and profitability of soybean at varying planting methods and nitrogen levels

A field experiment was conducted to study the effect of different planting methods (Happy Seeder sowing, Straw Chopper + Zero Tillage sowing, and conventional sowing) and nitrogen (N) levels (0%, 75%, 100%, and 125% of recommended N) on the emergence, growth, symbiotic parameters, productivity, and profitability of soybean sown after wheat harvest. Growth and symbiotic parameters were significantly better under Happy Seeder sowing and Straw Chopper + Zero Tillage sowing than conventional sowing. The seed yield, nutrient uptake, and economic returns were significantly higher under Happy Seeder sowing than other methods. The growth parameters, symbiotic parameters, biological, straw, and seed yields were increased significantly up to 100% recommended N level. The nutrient uptake increased significantly up to 100% recommended N level. Therefore, sowing with Happy Seeder after combine harvested wheat along with 100% recommended N would best optimize soybean yield and profitability.     

Trade-offs between on-farm varietal diversity and highly client-oriented breeding — a case study of upland rice in India

On-farm varietal diversity is now highest in marginal agricultural environments because, unlike the case in more favourable areas, modern varieties have not been a sufficiently attractive option for farmers to replace their landraces. However, the continued survival of landraces on farm is dependent on the continuing failure of plant breeding to provide better alternatives. Highly client-oriented breeding can produce suitable modern varieties for areas that were dominated by landraces. We examine here the case of the adoption of two upland rice varieties in three states in eastern India, Jharkhand, West Bengal and Orissa, where our surveys had confirmed low adoption of modern varieties in the upland ecosystem. The two new upland varieties were readily accepted by farmers who rapidly adopted them on large proportions of their land. On-farm diversity is maintained by the need to trade-off among varieties but once a variety with overall superiority was found this incentive was removed. The new varieties from the client-oriented breeding did not have weaknesses that farmers had to trade-off against their landraces so they were more likely to replace them. They also replaced older modern varieties. Farmers had previously maintained them along with landraces because they had to trade-off the higher yield of Kalinga III against the more stable yield of landraces or the higher yield of Vandana against the higher gain quality of the landraces. Only mean count per household could be used to test the significance of the differences between individual years. In all states, this revealed a significant reduction in landrace diversity with the adopting farmers when the addition of the two new varieties was not considered. Trends across years for mean varietal count, total count and Shannon–Wiener index showed a significant decline in Orissa, irrespective of whether the two new varieties were included in the analysis or not. In Jharkhand there was a significant decline only for mean count when the new varieties were not included. In Orissa, it was possible to test if rare landraces were as readily replaced as more common ones. Landrace replacement was unmitigated by increasing rarity yet the most rare landraces have the highest priority for genetic conservation. Some landraces were completely replaced by the farmers in the sample despite a diverse variety portfolio being a risk-reducing strategy in a region where there is a high risk of crop failure. There was little environmental heterogeneity in the marginal, drought-prone areas to slow this decline. The new varieties had an impact on the farming system because sometimes farmers brought additional upland into cultivation. They also introduced these varieties into more favourable, medium land. The strategy of releasing two new upland varieties met with some success in maintaining diversity.     

Feeding potential of <Emphasis Type="Italic">Cryptolaemus montrouzieri</Emphasis> against the mealybug <Emphasis Type="Italic">Phenacoccus solenopsis</Emphasis>

Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) is an exotic species native to the USA, damaging cotton and other plant families. The feeding potential of different development stages of Cryptolaemus montrouzieri Mulsant, a biological control agent against mealybugs, was investigated on different development stages of P. solenopsis. Fourth instar grubs and adults of C. montrouzieri were the most voracious feeders on different instars of mealybug. The number of 1^st instar nymphs of mealybug consumed by 1^st, 2^nd, 3^rd and 4^th instar larvae and adult beetles of C. montrouzieri was 15.56, 41.01, 125.38, 162.69 and 1613.81, respectively. The respective numbers of 2^nd and 3^rd instar nymphs of mealybug consumed were 11.15 and 1.80, 26.35 and 6.36, 73.66 and 13.32, 76.04 and 21.16, 787.95 and 114.66. The corresponding figures for adult female mealybugs were 0.94, 3.23, 8.47, 12.71 and 73.40, respectively. The results indicate that C. montrouzieri has the potential to be exploited as a biocontrol agent in North India; inoculative releases of 4^th instar larvae and adults may provide instant control of P. solenopsis. Field experiments should be conducted to determine the efficiency of the ladybird on this mealybug.     

Analysis of residuals for stability assessment of rice genotypes

The analysis of residuals computes general adaptabilities (GAs) and specific adaptabilities (SAs) of genotypes similar to combining ability analysis. The residual analysis is simple and robust being based on the first-degree statistics, and is assumption-free. A unique statistic of ratio of variances (VR) of residuals for individual genotypes allows comparing their stability. The residuals analysis of genotype × environment (GE) interactions was performed for grain yield (t ha^?1) of 25 rice (Oryza sativa L.) genotypes, including two developed by marker-assisted selection for root traits quantitative trait loci (QTL), tested across 16 sites. Results were compared with the linear regression analysis for (i) full set of 16 sites showing adequacy of linear model and (ii) subset of nine-poor sites showing inadequacy of linear model. There was agreement between the two analyses for situation (i) but not for situation (ii) when the regression analysis fails because of nonlinearity but the residual analysis retains its validity.     

Cytoplasmic differentiation using near-isonuclear polycytoplasmic male sterile lines in pearl millet

Summary Five near-isonuclear polycytoplasmic versions of 81A₁ and two of Pb 402A₃ male sterile lines of pearl millet (Pennisetum typhoides), along with their corresponding maintainer lines (81B and Pb 402B) were studied for 14 agronomic and two disease traits, and for isozymes of peroxidase in anthers and leaves for assessing cytoplasmic differences. Significant differences among isonuclear polycytoplasmic lines of both 81A₁ and Pb 402A₃, having the same genome and variable cytoplasms, were observed for several agronomic traits. Banding pattern of peroxidase isozymes revealed clear cut differences among cytoplasms. The results provide evidence for the influence of cytoplasmic factors on the phenotypic expression of nuclear genes.     

Number of crosses and population size for participatory and classical plant breeding

In the breeding of self-pollinating crops, crossing creates variation upon which selection is exerted. If the value of crosses cannot be predicted then this uncertainty means that many crosses need to be made. However, since there is a limit to the capacity of a breeding programme, more numerous crosses result in each cross having a small population size, fewer progenies in later generations and a lower probability of recovering good genotypes from each cross. Published theory on the optimum number of crosses in a plant breeding programme, for a predominantly self-pollinating crop, usually assumes that all crosses are equal value. This overestimates the number of crosses required. When the optimum size of a population in a favourable cross is considered, theory predicts that very large populations are desirable. The required population size is even larger if linkage of loci controlling different traits is also considered. Hence, in an inbreeding crop, one possible strategy is to select a small number of crosses that are considered favourable and produce large populations from them to increase the probability of recovering superior genotypes. In an out breeding crop, the analogy is a few composites with large population sizes. This low-cross-number strategy is ideally suited to the particular constraints and advantages of participatory plant breeding. Such an approach, although not essential, may still be advantageous in classical breeding. When a breeding programme is based on few crosses, which parents are chosen is crucial and farmer participatory methods are highly effective in narrowing the choice. Modified bulk population breeding methods, and recurrent selection are desirable strategies in the participatory plant breeding of self-pollinating crops when combined with a low-cross-number approach. This revised version was published online in August 2006 with corrections to the Cover Date.     

Description and efficacy of a response-based “QUAD” cyclical hypofractionated palliative-intent radiation protocol in dogs with macroscopic solid tumours: 108 cases

Palliative-intent radiation therapy can alleviate pain and clinical signs in dogs with cancer, but optimal fractionation scheme is unknown. The objective of this retrospective case series is to evaluate clinical benefit, objective response, adverse effects, and outcomes in 108 dogs with macroscopic solid tumours treated with a cyclical “QUAD” hypofractionated palliative-intent radiation therapy protocol. Median QUAD dose was 14 Gy (14–16 Gy). Median total dose was 28 Gy (14–48 Gy). Clinical benefit rate was 93%, with median onset of subjective palliation 21 days after the first QUAD, lasting a median of 134 days. Tumour volumetric objective response was assessed with CT prior to the third QUAD in 36 dogs, with stable disease in 24 dogs (67%) and partial response in 9 dogs (25%). Sinonasal and oral were the most common tumour locations in 32 and 30 dogs, respectively. Median progression-free survival was 153 days (95% CI 114–200). Median overall survival was 212 days (95% CI 152–259). Number of QUAD cycles completed, clinical benefit achieved, anti-inflammatory received, total radiation dose, time to maximum clinical benefit, and response duration were positively associated with progression-free and overall survival. Acute toxicities were observed in 15 dogs (14%) with 3 high-grade (grade 3) toxicities (3%). Low-grade (grade 1 and 2) late skin and ocular toxicities were observed in 31 dogs (29%), predominantly leukotrichia, alopecia, keratoconjunctivitis sicca, and cataracts. This report demonstrates that QUAD radiation is an alternative protocol to be considered for palliation of dogs with inoperable or advanced stage solid tumours.