Two latent variable risk assessment approaches for mixed continuous and discrete outcomes from developmental toxicity data

Measurements of both continuous and discrete outcomes are encountered in many statistical problems. Here we consider the particular context of teratology studies, where quantitative risk asessment is aimed at determining the effect of dose on the probability that an individual fetus is malformed or of low birth weight, both being important measures of teratogenicity. We will introduce two different joint marginal mean models for outcomes of a mixed nature. First, we propose the Plackett-Dale approach, where for each binary outcome it is assumed that there exists an underlying glatent variable. The latent malformation outcomes are then assumed to follow a Plackett distribution. The second approach we consider is a probit approach. Here it is assumed that there exists an underlying continuous variable for each binary outcome, so the joint distribution for weight and malformation can be assumed to follow a multivariate normal distribution. In both cases, specification of the full distribution will be avoided using pseudolikelihood and generalized estimating equations methodology, respectively. Quantitative risk assessment is illustrated using data from two developmental toxicology experiments.     

The optimal lignin quantification method to breed for an improved cell wall digestibility in perennial ryegrass

Perennial ryegrass (Lolium perenne) is an important source of protein and energy for dairy cattle. To improve the protein/energy ratio of this forage, focus is now on improving its cell wall digestibility. The in vitro assessment of the digestible fraction of the neutral detergent fibre (NDFD) is a superior method for determining the cell wall digestibility, but requires the use of ruminal fluid, which has a highly variable composition and is often not readily available. As lignin is considered the main cell wall component that impedes NDFD, we investigated whether this “subtrait” could serve as alternative breeding selection criterion to improve NDFD. Therefore, we assessed the accuracy of two lignin quantification methods: van Soest (ADL) and Klason lignin (KL). We also considered KL estimates corrected for the solubilized lignin (total lignin or TL) and non‐solubilized protein (TL'). Although the latter is considered the truest possible lignin content, it was not always the most correlated to NDFD, due to the limited accuracy of protein quantification on lignin residue. TL is most correlated to NDFD and we therefore recommend it for use in conventional breeding if NDFD determination is not a possibility. However, NDFD is still a superior selection criterion, as it combines the effect of several subtraits and not just lignin. For marker–trait association studies, a more accurate estimate of lignin content is more important than a high correlation with NDFD, but also here, TL performs best.     

Analysis of population structure and genetic diversity reveals gene flow and geographic patterns in cultivated rice (<Emphasis Type="Italic">O. sativa</Emphasis> and <Emphasis Type="Italic">O. glaberrima</Emphasis>) in West Africa

To fully exploit the diversity in African rice germplasm and to broaden the gene pool reliable information on the population genetic diversity and phenotypic characteristics is a prerequisite. In this paper, the population structure and genetic diversity of 42 cultivated African rice (Oryza spp.) accessions originating from West Africa (Benin, Mali and Nigeria, Liberia etc.) were investigated using 20 simple sequence repeats (SSR) and 77 amplified fragment length polymorphisms (AFLP). Additionally, field trials were set up to gain insight into phenotypic characteristics that differentiate the genetic populations among rice accessions. The analysis revealed considerably high polymorphisms for SSR markers (PIC mean?=?0.78) in the germplasm studied. A significant association was found between AFLP markers and geographic origin of rice accessions (R?=?0.72). Germplasm structure showed that Oryza sativa accessions were not totally isolated from Oryza glaberrima accessions. The results allowed identification of five O. glaberrima accessions which grouped together with O. sativa accessions, sharing common alleles of 18 loci out of the 20 SSR markers analyzed. Population structure analysis revealed existence of a gene flow between O. sativa and O. glaberrima rice accessions which can be used to combine several interesting traits in breeding programs. Further studies are needed to clarify the contributions of this gene flow to valuable traits such as abiotic and biotic stresses including disease resistance.     

Fusarium head blight (FHB) in Flanders: population diversity, inter-species associations and DON contamination in commercial winter wheat varieties

The presence of Fusarium spp. causing Fusarium head blight (FHB) of wheat was studied in Flanders (Belgium) in 2007 and 2008. Symptoms, deoxynivalenol content (DON), Fusarium spp. and trichothecene chemotypes were determined at seven locations on different commercial wheat varieties. Overall, significant differences in disease pressure between locations and varieties were observed within 1 year. In addition, we were able to detect consistent and significant resistance differences among the common varieties both under high disease pressure (2007) and low disease pressure (2008). The accumulation of DON was not related to the presence of F. graminearum but showed a clear correlation with rainfall during and after the period of anthesis. During the two-year survey, characterisation of 756 Fusarium samples by species-specific PCR designated F. poae and F. graminearum as the predominant species in Flanders. Furthermore, most of the ears were colonised by multiple FHB pathogens in 2007 whereas the Fusarium population was less complex in 2008. Log-linear analysis of these multiple (two- and three-way) species interactions revealed a clear correlation between F. poae and several pathogens of the FHB disease complex. Finally, chemotype analysis showed that F. culmorum and F. graminearum were respectively of the NIV chemotype and DON chemotype. 3-ADON and 15-ADON chemotypes occurred in more or less equal amounts within the F. graminearum population both in 2007 and 2008. The congruence of these results with observations throughout Europe are discussed.     

The non-linear effect (determined by the penalised partial-likelihood approach) of milk-protein concentration on time to first insemination in Belgian dairy cows

The time to first insemination in dairy cows depends partly on the energy balance of the cow. Because milk-protein concentration is related to the energy balance, we investigated whether milk-protein concentration predicted the hazard of being inseminated. The main objective of the paper is to demonstrate that the relationship between milk-protein concentration and the hazard of being inseminated was not linear and that this non-linear relationship was modelled adequately using cubic–splines. The semiparametric Cox model was used to introduce protein concentration into the model as a time-varying covariate and additionally herd was added to the model as a frailty term to adjust for the clustering of the cows within a herd. We extended the penalised partial-likelihood technique to fit the frailty model with cubic–splines for the effect of the protein concentration. The model was fitted for a large database consisting of 5114 multiparous cows from 181 different farms. Low milk-protein concentration (<2.7%) was associated with a negative energy balance and this probably led to the decreased hazard. On the other hand, high milk-protein concentration (>4.0%) was linked with low milk production and it was probably a farmer’s decision not to inseminate such cows, leading to the observed decreased hazard.     

Short-term effects of energy changes on plasma leptin concentrations and glucose tolerance in healthy ponies

To determine whether plasma leptin concentrations and glucose tolerance are affected by changes in energy balance, nine healthy Shetland ponies were fed at 140% followed by 75% of their maintenance requirements for 13 days in each of the two periods. Bodyweight was recorded every three days. Blood samples were taken every two days and analysed for leptin and cortisol. An oral glucose tolerance test was performed on day 7 of each period. Serial blood samples were analysed for glucose and insulin. Although bodyweight was not affected, plasma leptin concentrations increased (P<0.001) initially during overfeeding, but returned to previous values after 7 days. During underfeeding, plasma leptin concentrations decreased (P<0.001). Underfeeding was associated with a higher AUC for plasma glucose (P=0.02) and plasma insulin (P=0.05) resulting in a decreased glucose tolerance (AUC glucose/AUC insulin; P=0.008), probably due to a plasma cortisol increase caused by the reduced feed intake. It is concluded that changes in energy balance, without altering bodyweight, can influence plasma leptin concentrations in ponies.     

Effect of the 1BL.1RS translocation and of the Glu-B3 variation on fifteen quality tests in a doubled haploid population of wheat (Triticum aestivum L.)

To investigate the impact of 1BL.1RS translocation on protein content, starch quality, dough rheology, RMT volumes and other quality traits, a doubled haploid population was created and sown in a two-year field experiment. Translocated genotypes accumulated more proteins in the endosperm than non-translocated genotypes. Decrease in the gelatinization of starch was associated with the 1BL.1RS translocation. As for rheological parameters, adapted to bread types not requiring high mixing energy, the 1BL.1RS translocation significantly reduced the elasticity, tenacity and strength of the dough compared to allele c of Glu-B3. Tolerance to over-mixing was also significantly lower in translocated DH lines. In contrast to previously published work, the presence of allele Glu-D3 c resulted in significantly higher tenacity, and thus strength, compared with the allele Glu-D3 b in the present DH population. The final baking test performed on the DH lines of the population, combining favourable alleles for dough rheology and high protein content, demonstrated that in some cases lower tenacity induced by the 1BL.1RS translocation or by Glu-B3 b increases the volume of the loaves.     

Management Processes on Two Small-Holder Sprinkler Layouts: A Case Study from Zimbabwe

Management patterns on two sprinkler schemes forsmall-holders are compared. The one overridingdifference is in the layout – soils, crops, climate,altitude, plot size, source of water and hardwarebeing similar or identical. Both schemes are used bysmall-holders to grow vegetables for cash. One layoutallows for individual control over both crop choiceand water application, and requires one group meetingeach month, to set the fee for the payment of theelectricity bill for the pump-set. The other layout,copied from Zimbabwe's large farms, is shown to imposegroup decision making on the choice of crop andvariety, the area to be planted and the planting date,forcing farmers to hold 17 meetings between July 31stand November 23rd. The case study shows the impact ofthe layout of the hardware on the managementprocess.