Geographical partitioning of goat diversity in Europe and the Middle East

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.

Impact of variation in acute virulence of BVDV1 strains on design of better vaccine efficacy challenge models

Due to antigenic differences between BVDV1 and BVDV2 strains, both pestivirus species are included in U.S. vaccines. The efficacy of these vaccines in preventing acute infections is evaluated based on reduction of clinical disease. While high virulence BVDV2 strains are used in U.S. vaccine efficacy studies, the BVDV1 strain used (NY-1) produces very little in the way of clinical disease. In order to identify a BVDV1 strain that generates a more pronounced clinical presentation, three field strains were compared to NY-1. Infection with two of the field strains resulted in significantly more pronounced clinical disease compared to NY-1. Decreasing the inoculation of a field strain by two logs did not significantly change clinical presentation.

Effects of variation in nest curtain design on pre-laying behaviour of domestic hens

Laying hens in loose-housing systems select a nest daily in which to lay their eggs among many identical looking nests, they often prefer corner nests. We investigated whether heterogeneity in nest curtain appearance – via colours and symbols – would influence nest selection and result in an even distribution of eggs among nests. We studied pre-laying behaviour in groups of 30 LSL hens across two consecutive trials with eight groups per trial. Half of the groups had access to six identical rollaway group-nests, while the others had access to six nests of the same type differing in outer appearance. Three colours (red, green, yellow) and three black symbols (cross, circle, rectangle) were used to create three different nest curtain designs per pen. Nest position and the side of entrance to the pens were changed at 28 and 30 weeks of age, respectively, whereby the order of changes was counterbalanced across trials. Nest positions were numbered 1–6, with nest position 1 representing the nest closest to the pen entrance. Eggs were counted per nest daily from week of age 18 to 33. Nest visits were recorded individually with an RFID system for the first 5 h of light throughout weeks 24–33. Hens with access to nests differing in curtain appearance entered fewer nests daily than hens with identical nests throughout the study but both groups entered more nests with increasing age. We found no other evidence that curtain appearance affected nest choice and hens were inconsistent in their daily nest selection. A high proportion of eggs were laid in corner nests especially during the first three weeks of lay. The number of visits per egg depended upon nest position and age: it increased with age and was higher after the nest position change than before in nest position 1, whereas it stayed stable over time in nest position 6. At 24 weeks of age, gregarious nest visits (hens visiting an occupied nest when there was at least one unoccupied nest) and solitary nest visits (hens visiting an unoccupied nest when there was at least one occupied nest) accounted for a similar amount of nest visits, however, after the door switch, gregarious nest visits made up more than half of all nest visits, while the number of solitary nest visits had decreased. The visual cues were too subtle or inadequate for hens to develop individual preferences while nest position, entrance side, age and nest occupancy affected the quantity and type of nest visits.

The role of landuse and natural determinants for grassland vegetation composition in the Swiss Alps

The Alps provide a high habitat diversity for plant species, structured by broad- and fine-scale abiotic site conditions. In man-made grasslands, vegetation composition is additionally affected by the type of landuse. We recorded vegetation composition in 216 parcels of grassland in 12 municipalities representing an area of 170 x 70 km in the south-eastern part of the Swiss Alps. Each parcel was characterized by a combination of altitudinal level (valley, intermediate, alp). traditional landuse (mown. grazed), current management (mown, grazed, abandoned). and Fertilization (unfertilized, fertilized). For each parcel we also assessed the abiotic factors aspect, slope, pH value, and geographic coordinates, and for each municipality annual precipitation and its cultural tradition. We analysed vegetation composition using (i) variation partitioning in RDA. (ii) cover of graminoids. non-legume forbs, and legumes, and (iii) dominance and frequency of species. Species composition was determined by, in decreasing order of variation explained. landuse, broad-scale abiotic factors, fine-scale abiotic factors. and cultural tradition. Current socio-economically motivated landuse changes, such as grazing of unfertilized former meadows or their abandonment, strongly affect vegetation composition. In our study, the frequency of characteristic meadow species was significantly smaller in grazed and even smaller in abandoned parcels than in still mown ones, suggesting less severe consequences of grazing for vegetation composition than of abandonment. Therefore. low-intensity grazing and mowing every few years should be considered valuable conservation alternatives to abandonment. Furthermore. because each landuse type was characterized by different species. a high variety of landuse types should be promoted to preserve plant species diversity in Alpine grasslands. (C) 2007 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.

Isotopes Trace Biogeochemistry and Sources of Cu and Zn in an intertidal soil

River floodplain soils are sinks and potential sources for toxic trace metals like Cu and Zn. We hypothesize that stable Cu and Zn isotope ratios reflect both the mobilization and the sources of metals. We determined the soil properties, the concentrations and partitioning of Cu and Zn, and variations in δ65Cu and δ66Zn values in a core obtained from an Aquic Udifluvent developed on a freshwater intertidal mudflat of the River Elbe, Germany. The core was sampled at 2 cm intervals to a depth of 34 cm, which corresponds to approximately 9 yr of sedimentation. Elevated concentrations of Cu (up to 320 μg g−1) and Zn (up to 2080 μg g−1) indicated anthropogenic pollution. At the time of sampling the redox conditions changed from oxic (Eh 200 to 400 mV, above 22 cm deep) to strongly anoxic conditions (-100 to -200 mV, below 22 cm deep). The δ65Cu values varied systematically with depth (from -0.02 to 0.16‰) and were correlated with the Fe, C, and N concentrations. Although pre-depositional variations cannot be ruled out, the systematic variation with depth suggests post-sedimentation fractionation of δ65Cu in response to seasonally variable organic matter deposition and redox conditions. In contrast, the δ66ZnIRMM values were uniform (from -0.07 to 0.01‰) throughout the core, indicating that the Zn isotopes did not significantly fractionate after deposition and that the Zn sources were homogeneous throughout the sedimentation.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

Biological variation of established and novel biomarkers for atherosclerosis: Results from a prospective, parallel-group cohort study.

BACKGROUND Biomarkers are a promising tool for the management of patients with atherosclerosis, but their variation is largely unknown. We assessed within-subject and between-subject biological variation of biomarkers in peripheral artery disease (PAD) patients and healthy controls, and defined which biomarkers have a favorable variation profile for future studies. METHODS Prospective, parallel-group cohort study, including 62 patients with stable PAD (79% men, 65±7years) and 18 healthy control subjects (44% men, 57±7years). Blood samples were taken at baseline, and after 3-, 6-, and 12-months. We calculated within-subject (CVI) and between-subject (CVG) coefficients of variation and intra-class correlation coefficient (ICC). RESULTS Mean levels of D-dimer, hs-CRP, IL-6, IL-8, MMP-9, MMP-3, S100A8/A9, PAI-1, sICAM-1, and sP-selectin levels were higher in PAD patients than in healthy controls (P≤.05 for all). CVI and CVG of the different biomarkers varied considerably in both groups. An ICC≥0.5 (indicating moderate-to-good reliability) was found for hs-CRP, D-Dimer, E-selectin, IL-10, MCP-1, MMP-3, oxLDL, sICAM-1 and sP-selectin in both groups, for sVCAM in healthy controls and for MMP-9, PAI-1 and sCD40L in PAD patients. CONCLUSIONS Single biomarker measurements are of limited utility due to large within-subject variation, both in PAD patients and healthy subjects. D-dimer, hs-CRP, MMP-9, MMP-3, PAI-1, sP-selectin and sICAM-1 are biomarkers with both higher mean levels in PAD patients and a favorable variation profile making them most suitable for future studies.

Variability of lung function predicts loss of asthma control following withdrawal of inhaled corticosteroid treatment

BACKGROUND One aspect of a multidimensional approach to understanding asthma as a complex dynamic disease is to study how lung function varies with time. Variability measures of lung function have been shown to predict response to beta(2)-agonist treatment. An investigation was conducted to determine whether mean, coefficient of variation (CV) or autocorrelation, a measure of short-term memory, of peak expiratory flow (PEF) could predict loss of asthma control following withdrawal of regular inhaled corticosteroid (ICS) treatment, using data from a previous study. METHODS 87 adult patients with mild to moderate asthma who had been taking ICS at a constant dose for at least 6 months were monitored for 2-4 weeks. ICS was then withdrawn and monitoring continued until loss of control occurred as per predefined criteria. Twice-daily PEF was recorded during monitoring. Associations between loss of control and mean, CV and autocorrelation of morning PEF within 2 weeks pre- and post-ICS withdrawal were assessed using Cox regression analysis. Predictive utility was assessed using receiver operator characteristics. RESULTS 53 out of 87 patients had sufficient PEF data over the required analysis period. The mean (389 vs 370 l/min, p<0.0001) and CV (4.5% vs 5.6%, p=0.007) but not autocorrelation of PEF changed significantly from prewithdrawal to postwithdrawal in subjects who subsequently lost control, and were unaltered in those who did not. These changes were related to time to loss of control. CV was the most consistent predictor, with similar sensitivity and sensitivity to exhaled nitric oxide. CONCLUSION A simple, easy to obtain variability measure of daily lung function such as the CV may predict loss of asthma control within the first 2 weeks of ICS withdrawal.

Test-retest reliability of the nociceptive withdrawal reflex and electrical pain thresholds after single and repeated stimulation in patients with chronic low back pain

Recent studies have shown that the nociceptive withdrawal reflex threshold (NWR-T) and the electrical pain threshold (EP-T) are reliable measures in pain-free populations. However, it is necessary to investigate the reliability of these measures in patients with chronic pain in order to translate these techniques from laboratory to clinic. The aims of this study were to determine the test-retest reliability of the NWR-T and EP-T after single and repeated (temporal summation) electrical stimulation in a group of patients with chronic low back pain, and to investigate the association between the NWR-T and the EP-T. To this end, 25 patients with chronic pain participated in three identical sessions, separated by 1 week in average, in which the NWR-T and the EP-T to single and repeated stimulation were measured. Test-retest reliability was assessed using intra-class correlation coefficient (ICC), coefficient of variation (CV), and Bland-Altman analysis. The association between the thresholds was assessed using the coefficient of determination (r (2)). The results showed good-to-excellent reliability for both NWR-T and EP-T in all cases, with average ICC values ranging 0.76-0.90 and average CV values ranging 12.0-17.7%. The association between thresholds was better after repeated stimulation than after single stimulation, with average r (2) values of 0.83 and 0.56, respectively. In conclusion, the NWR-T and the EP-T are reliable assessment tools for assessing the sensitivity of spinal nociceptive pathways in patients with chronic pain.

A multi-center study: Intra-scan and inter-scan variability of diffusion spectrum imaging

The objective of this study was to investigate whether it is possible to pool together diffusion spectrum imaging data from four different scanners, located at three different sites. Two of the scanners had identical configuration whereas two did not. To measure the variability, we extracted three scalar maps (ADC, FA and GFA) from the DSI and utilized a region and a tract-based analysis. Additionally, a phantom study was performed to rule out some potential factors arising from the scanner performance in case some systematic bias occurred in the subject study. This work was split into three experiments: intra-scanner reproducibility, reproducibility with twin-scanner settings and reproducibility with other configurations. Overall for the intra-scanner and twin-scanner experiments, the region-based analysis coefficient of variation (CV) was in a range of 1%-4.2% and below 3% for almost every bundle for the tract-based analysis. The uncinate fasciculus showed the worst reproducibility, especially for FA and GFA values (CV 3.7-6%). For the GFA and FA maps, an ICC value of 0.7 and above is observed in almost all the regions/tracts. Looking at the last experiment, it was found that there is a very high similarity of the outcomes from the two scanners with identical setting. However, this was not the case for the two other imagers. Given the fact that the overall variation in our study is low for the imagers with identical settings, our findings support the feasibility of cross-site pooling of DSI data from identical scanners.