Efficiency of using spatial analysis in first-generation coastal Douglas-fir progeny tests in the US Pacific Northwest

Single-trial and across-trial spatial analyses using autoregressive error structures were conducted for growth traits based on 1,146 data sets from 275 Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] progeny trials in 45 first-generation breeding zones in the US Pacific Northwest. The breeding zones encompassed a wide range of latitude, longitude, and elevation. Efficiency of using spatial analysis in reducing variation due to site heterogeneity, estimating genetic parameters, and increasing prediction accuracy was compared among different experimental designs, traits, assessment ages, and tree spacings. More than 97% of the data sets showed significant model improvement with spatial analysis, and height showed more improvement than diameter or volume. Spatial analysis on average removed 14~34% of residual variance due to spatial heterogeneity, which resulted in an up to 20% increase in accuracy of breeding value prediction. The coefficient of variation decreased substantially due to spatial adjustment. Rank correlation between predicted gains before and after spatial analysis was about 0.96, and spatial analysis had little effect on the average predicted gain of the top 20% of parents. We did not observe substantial geographic trends in improvements due to spatial adjustment. Across-site spatial analysis had almost no effect on genotype-by-environment interaction but tended to increase among-trial heterogeneity of residual variance. Two different methods for across-trial spatial analysis were compared and discussed.     

Effects of seven potential probiotic strains on specific immune responses in healthy adults: a double-blind, randomized, controlled trial

This pilot study investigated the immunomodulatory properties of seven probiotic strains. Eighty-three healthy volunteers aged 18-62 years consumed 2 x 10(10) CFU of bacteria or a placebo (maltodextrin) over 3 weeks (D0-D21). Subjects received an oral cholera vaccine at D7 and at D14; blood and saliva samples were collected at D0, D21 and D28. Serum samples were analyzed for specific IgA, IgG and IgM, and saliva samples were analyzed for specific IgA only, by ELISA. Statistical analyses were based on Wilcoxon's signed-rank test (intragroup analyses) and exact median t-test (intergroup analyses). Salivary analysis showed no difference in specific IgA concentrations between groups. Serum analysis indicated an effect of some of the tested strains on specific humoral responses. Between D0 and D21, IgG increased in two probiotic groups, for example, Bifidobacterium lactis Bl-04 and Lactobacillus acidophilus La-14, compared with controls (P=0.01). Trends toward significant changes in immunoglobulin serum concentrations compared with controls (P<0.1) were found for six out of the seven probiotic strains. In conclusion, some strains of probiotics demonstrated a faster immune response measured with serum immunoglobulin indicators, especially IgG, although overall vaccination was not influenced. Specific strains of probiotics may thus act as adjuvants to the humoral immune response following oral vaccination.     

Field release of genetically marked Azospirillum brasilense in association with Sorghum bicolor L.

The agronomic impact of genetically tagged azospirilla (Azospirillum brasilense)was assessed in open field and their fluctuation were monitored in the soil/rhizosphere. Strain performance, upon inoculation of sorghum, was evaluated over a two-years period; agronomic treatments included nitrogen application (0, 80, 160 kg ha^–1), and types of inoculant (Sp245 lacZ, Sp6 gusA, Sp6 IAA⁺⁺ gusA). Grain yield was higher for inoculated seed plots than in non-inoculated ones, whereas nitrogen content, biomass of plant residues and nitrogen in plant residues gave values that were not statistically different. Root length density (RLD) of sorghum at the end of the stem elongation stage was affected only by the indole-3-acetic acid (IAA) overproducer Azospirillum strain (A. brasilense Sp6 IAA⁺⁺ gusA) with respect to the normal IAA producer (A. brasilense Sp6 gusA), being higher in the first 40 cm of depth, notwithstanding the level of nitrogen fertilization. The traceability of the released genetically modified strains enabled to monitor their ability to colonise soil and roots. Moreover, the genetic modification per se vs. the non-modified counterpart, did not affect the culturable aerobic population in soil, microfungi, streptomycetes, fluorescent pseudomonads, soil microbial biomass, or some microbial activities, all selected as important indicators.     

Relative efficiency of unequal versus equal cluster sizes in cluster randomized trials using generalized estimating equation models

There is growing interest in conducting cluster randomized trials (CRTs). For simplicity in sample size calculation, the cluster sizes are assumed to be identical across all clusters. However, equal cluster sizes are not guaranteed in practice. Therefore, the relative efficiency (RE) of unequal versus equal cluster sizes has been investigated when testing the treatment effect. One of the most important approaches to analyze a set of correlated data is the generalized estimating equation (GEE) proposed by Liang and Zeger, in which the “working correlation structure” is introduced and the association pattern depends on a vector of association parameters denoted by ρ. In this paper, we utilize GEE models to test the treatment effect in a two‐group comparison for continuous, binary, or count data in CRTs. The variances of the estimator of the treatment effect are derived for the different types of outcome. RE is defined as the ratio of variance of the estimator of the treatment effect for equal to unequal cluster sizes. We discuss a commonly used structure in CRTs—exchangeable, and derive the simpler formula of RE with continuous, binary, and count outcomes. Finally, REs are investigated for several scenarios of cluster size distributions through simulation studies. We propose an adjusted sample size due to efficiency loss. Additionally, we also propose an optimal sample size estimation based on the GEE models under a fixed budget for known and unknown association parameter (ρ) in the working correlation structure within the cluster.     

Preventive study in subjects at risk of fatal familial insomnia: Innovative approach to rare diseases

Abstract

The text describes a preventive clinical trial with drug treatment in a very rare neurodegenerative disease (Fatal familial Insomnia, FFI) designed with the help of individuals at genetic risk of developing the disease, asymptomatic carriers, who have agreed to be exposed over a 10-year period to doxycycline, an antibiotic with anti-prion activity. At least 10 carriers of the FFI mutation over 42 y old will be treated with doxycycline (100 mg/die) and the incidence of the disease will be compared to that of an historical dataset. For ethical reasons a randomized, double-blind, placebo-controlled trial was not feasible, however the study design and the statistical analysis ensure the scientific value of the results. This approach might represent an important breakthrough in terms of potential therapy and knowledge of rare diseases that could give some hopes to these neglected patients.     

Field observations of the effect of Metarhizium anisopliae var. acridum on the saxaul locust,Dericorys albidula Serville (Orthoptera: Dericorythidae)

Dericorys albidula Serville (Orthoptera: Dericorythidae) is a major pest of Haloxylon ammodendron and other saxaul plant species in the Qom province, Iran. Using fungal insecticides can be an alternative method for chemical insecticides. Effect of insecticide fungi, Metarhizium anisopliae var. acridum, on the various nymphs of D. albidula was studied in the field through 2005 and 2006. Fixed concentrations of fungi (10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰ and 10¹³ spore mL^?1) were prepared as gasoline formulation and were sprayed on the locusts on H. ammodendron trees, and mortality percentage was recorded 15 days after treatment. The results showed that various concentrations significantly affected on the second, third, fourth and fifth nymphal instars of D. albidula compared to control in 2006, although this effect was lower in 2005 on nymphs. Mortality of the highest concentration (10¹³ spore mL^?1) was higher (17.6–24%) than other concentrations in all tests, but these values were not notable. The results of this study showed that using M. anisopliae var. acridum diluted in gasoline can be effective on nymphal instars of locust, D. albidula, in two continuous years.     

Peripheral-zone treatments for plum curculio management: validation in commercial apple orchards

A field trial was conducted using an oil formulation of the entomopathogenic fungus, Metarhizium flavoviride Gams & Rozyspal (Deuteromycotina: Hyphomycetes), to control the variegated grasshopper, Zonocerus variegatus L. (Orthoptera: Pyrgomorphidae). The influence of dispersal and secondary pick-up from the spray residue on mortality was assessed by sampling insects from the treated plots at intervals and monitoring disease levels during subsequent incubation in the laboratory. The cumulative mortality curves showed the pathogen to be highly effective, even in samples taken 8 days after spraying. A model was developed to link the influence of mortality, incubation, secondary pick-up of spores and insect dispersal, on the shape of these cumulative mortality curves. The model proved useful for data received from an experiment using small plot sizes, where insect dispersal is a big problem. The spray residue had an important influence on overall insect mortality. The model also indicated a difference in speed of kill between field and laboratory samples, suggesting an incubation delay in the field.