A local influence approach applied to binary data from a psychiatric study

Recently, a lot of concern has been raised about assumptions needed in order to fit statistical models to incomplete multivariate and longitudinal data. In response, research efforts are being devoted to the development of tools that assess the sensitivity of such models to often strong but always, at least in part, unverifiable assumptions. Many efforts have been devoted to longitudinal data, primarily in the selection model context, although some researchers have expressed interest in the pattern-mixture setting as well. A promising tool, proposed by Verbeke et al. (2001, Biometrics 57, 43-50), is based on local influence (Cook, 1986, Journal of the Royal Statistical Society, Series B 48, 133-169). These authors considered the Diggle and Kenward (1994, Applied Statistics 43, 49-93) model, which is based on a selection model, integrating a linear mixed model for continuous outcomes with logistic regression for dropout. In this article, we show that a similar idea can be developed for multivariate and longitudinal binary data, subject to nonmonotone missingness. We focus on the model proposed by Baker, Rosenberger, and DerSimonian (1992, Statistics in Medicine 11, 643-657). The original model is first extended to allow for (possibly continuous) covariates, whereafter a local influence strategy is developed to support the model-building process. The model is able to deal with nonmonotone missingness but has some limitations as well, stemming from the conditional nature of the model parameters. Some analytical insight is provided into the behavior of the local influence graphs.     

Stability of interleukin 6, soluble interleukin 6 receptor,interleukin 10 and CC16 in human serum

The stability of interleukin 6 (IL-6), its soluble receptor (sIL-6R), IL-10 and CC16 or uteroglobin (an endogenous cytokine inhibitor) in human serum was examined using an accelerated stability testing protocol according to the Arrhenius equation. Further, the effect of time delay between blood sampling and sample processing, clotting temperature and repeated freeze-thaw cycles on serum levels of these proteins were determined. Paired serum samples were stored at 4 degrees C, 20 degrees C, 30 degrees C and 40 degrees C for 1 to 21 days. We found that IL-6 and CC16 concentrations did not change at 4 degrees C, 20 degrees C and 30 degrees C. Interleukin-6 concentrations significantly declined after 11 days at 40 degrees C. The concentrations of sIL-6R and IL-10 did not change at 4 degrees C but significantly decreased at 20 degrees C (after 21 and 14 days respectively), 30 degrees C and 40 degrees C (after 1 day at both temperatures for both cytokines). Arrhenius-plots indicated that sIL-6R and IL-10 are stable for at least several years at -20 degrees C and -70 degrees C, respectively. Since their relative stability, no Arrhenius-plot could be calculated for IL-6 and CC16. The concentrations of the proteins examined were not significantly altered by repeated freeze-thaw cycles, nor by extended clotting times at 4 degrees C or 20 degrees C. We conclude that serum samples for the determination of IL-6, sIL-6R and CC16 can be stored at -20 degrees C for several years, but for IL-10 determinations, storage at -70 degrees C is recommended.     

Evaluation of progesterone receptor expression in eosinophils using real-time quantitative PCR

Progesterone has been shown in many instances to have immune-suppressant activities. Most of these activities have been investigated in the light of general immune suppression or with a focus on lymphocytes. However, many clinical and in vitro studies have shown that progesterone also has a suppressive effect on eosinophilia. This effect so far has not been thoroughly investigated. The purpose of this study was to evaluate whether the effect is mediated via the classical progesterone receptor (PR). We developed a new real-time quantitative PCR (RQ-PCR) for the analysis and quantification of expression of the classical PR. The test was first validated both on breast cancer cell lines and on breast cancer biopsies. Subsequently, when using eosinophils isolated from peripheral blood of healthy volunteers, we could not find evidence for the expression of PR. These data suggest that the effects of progesterone on eosinophils are not mediated by the classical PR.     

Abnormal offspring following in vitro production of bovine preimplantation embryos: a field study

Data on 944 calves from 2228 in vitro-produced (IVP) bovine preimplantation embryos were compared with data on 2787 AI calves born in the same herds in 1995. Bovine preimplantation embryos were produced in vitro following ovum pick up (OPU) from donor cows and pregnant heifers in an open nucleus breeding program. After 7 d of in vitro culture on a BRL cell monolayer in the presence of 10% FCS, frozen-thawed expanded blastocysts and fresh morulae to expanded blastocysts were transferred into recipient heifers and cows at 119 contracted farms throughout the Netherlands. The pregnancy rate, as confirmed by palpation per rectum between 90 and 150 d after transfer was 43.5% for both fresh and frozen embryos. Data on IVP and AI calves were registered by the farmers. The percentage of calves with a congenital malformation and the percentage of male calves were related to the total number of calves born. Gestation length, birth weight (measured by a balance), perinatal mortality and ease of calving were analyzed in a subdataset (699 IVP and 2543 AI calves, respectively) by a comparative analysis of variance (ANOVA). The ANOVA model included herd, month of calving, sire nested within AI or IVP, parity and breed of the inseminated cow/embryo recipient, sex of calf, type of calf (AI or IVP) and two-way interactions between type of calf and sex, parity and breed. The percentage of calves with congenital malformations was 3.2% and 0.7% for IVP and AI calves, respectively. An increased incidence of hydro-allantois and abnormal spinal cords and limbs was observed in IVP calves. The percentage of male calves was significantly different between IVP and AI, 55.5% and 48.9%, respectively (Chi-square, 1 degree of freedom, P < 0.05). On the average, IVP calves showed a significant increase of birth weight by 10% (4-5 kg), a 3-d longer gestation period, 2.4% more perinatal mortality and a more difficult calving process compared to AI calves (P < 0.05). From these results it is concluded that calves produced by IVP deviate significantly from calves produced by AI.     

Current measures of nutrient resorption efficiency lead to a substantial underestimation of real resorption efficiency: facts and solutions

Nutrient resorption is an important process during leaf senescence, which helps plants to minimize nutrient losses. To quantify nutrient resorption, the parameter resorption efficiency is commonly used. This parameter describes the percentage of the nutrient pool withdrawn before leaf abscission. The nutrient pool is generally expressed on the basis of leaf mass or leaf area, assuming that these bases do not change during senescence. In this paper we firstly present a mathematical formula describing the effect of change in measurement basis on the difference between the real resorption efficiency (RRE) value and the measured resorption efficiency (MRE). This formula shows that even moderate senescence-related changes in a measurement basis can lead to considerable underestimation of RRE. Secondly, to estimate the general change in measurement basis we quantified leaf mass loss and leaf shrinkage during senescence from literature data. These data shows that mass loss percentages can be as high as 40%, and leaf shrinkage can be up to 20%. This level of change in basis seriously compromises the MRE when not corrected for. Using our formula and the reported average literature values of changes in leaf mass (21%) and leaf shrinkage (11%) during senescence, we calculated that the average RRE for nitrogen and phosphorous of terrestrial plants is 6% (leaf area) to 10% (leaf mass) higher than the 50%, respectively 52% as reported by Aerts (1996) . This implies that nutrient resorption from senescing leaves is even more important for nutrient retention in terrestrial plants than thought so far. We advocate that preselecting leaves and monitoring the measurement basis throughout the duration of the experiment should minimize the difference between MRE and RRE.     

Activated T cells complicate the identification of regulatory T cells in rheumatoid arthritis

Most cell surface markers for CD4⁺CD25⁺ regulatory T cells (Tregs) are also expressed by activated non-regulatory T cells. Recently, CD127 down-regulation was found to identify functional Tregs in healthy individuals, but there are no data from patients with inflammatory conditions. We examined peripheral blood mononuclear cells (PBMC) from rheumatoid arthritis patients with active inflammation and from healthy controls, and found that CD4⁺ T cells contained an equal proportion of CD25⁺CD127⁻/low cells in both groups. In patients, not all these cells expressed intracellular FOXP3. Upon activation by anti-CD3/anti-CD28, PBMC rapidly down-regulated CD127, while FOXP3 up-regulation was transitory and occurred in fewer cells. The activated cells were not anergic to restimulation and had no suppressive effects. The distinct kinetics indicate that the FOXP3⁻CD127⁻/low cells in rheumatoid arthritis patients most likely represent activated non-regulatory T cells. This complicates the use of CD127 for identification of Tregs in inflammatory diseases.     

Restoration of Dry Afromontane Forest Using Pioneer Shrubs as Nurse-Plants for Olea europaea ssp. cuspidata

Shrubs are often considered competitive barriers for seedlings planted in reforestation programs, although they can facilitate tree recruitment, especially in ecosystems under high abiotic stress. An alternative reforestation technique using pioneer shrubs as nurse‐plants for Olea europaea ssp. cuspidata was tested in exclosures in northern Ethiopia. Seedlings were planted in three different microhabitats, and their survival was monitored. The microhabitats were bare soil patches between shrubs, patches under the dominant shrub Acacia etbaica, and patches under Euclea racemosa, an evergreen shrub, which supports the majority of naturally established Olea recruits. The ability of shrubs to offer protection against browsing goats was tested experimentally. Controlled shading was used to determine whether solar irradiation causes seedling mortality in environments without water stress. Data were analyzed using Kaplan–Meier survival analysis, Kruskal–Wallis analysis of variance (ANOVA), and one‐way ANOVA. Olea survival was significantly higher and shoot damage by goats was lower when planted under shrub cover compared to bare soil patches, particularly under Euclea canopies, although high shade levels reduced seedling performance. Reduction of solar radiation by shrub canopies and thus control of soil–water evaporation and seedling transpiration most likely controlled the observed facilitation. Planting under shrubs may increase seedling survival and assist regeneration of dry Afromontane vegetation. Preserving pioneers also reduces soil erosion and conserves biodiversity. Excluding livestock is essential for Olea woodland restoration and allows persistent but morphologically modified Olea shrubs to develop vigorous regrowth. Facilitative processes are guiding principles for assisted forest restoration, but above‐average rains may be critical to restore higher biomass levels in semiarid areas.     

Jaw and hyolingual movements during prey transport in varanid lizards: effects of prey type

The ability to modulate feeding kinematics in response to prey items with different functional properties is likely a prerequisite for most organisms that feed on a variety of food items. Variation in prey properties is expected to reveal variation in feeding function and the functional role of the different phases in a transport cycle. Here we describe the kinematics of prey transport of two varanid species, Varanus niloticus and Varanus ornatus. These species were selected for analysis because of their highly specialised hyolingual system and food transport mechanism (inertial food transport). In these animals, tongue and hyoid movements are expected to make no, or only a minor, contribution to prey transport. We observed statistically significant prey type effects that could be associated with prey properties such as mass, size and mobility. These data show that both species are capable of modulating the kinematics of food transport in response to different prey types. Moreover, not only the kinematics of the jaws were modulated in response to prey characteristics but also the anterior/posterior movements of the tongue and hyoid. This suggests a more important role of the tongue and hyolingual movements in these animals than previously suspected. In contrast, head movements were rather stereotyped and were not modulated in response to changes in prey type.