A genetic and spatial Bayesian analysis of mastitis resistance

A nationwide health card recording system for dairy cattle was introduced in Norway in 1975 (the Norwegian Cattle Health Services). The data base holds information on mastitis occurrences on an individual cow basis. A reduction in mastitis frequency across the population is desired, and for this purpose risk factors are investigated. In this paper a Bayesian proportional hazards model is used for modelling the time to first veterinary treatment of clinical mastitis, including both genetic and environmental covariates. Sire effects were modelled as shared random components, and veterinary district was included as an environmental effect with prior spatial smoothing. A non-informative smoothing prior was assumed for the baseline hazard, and Markov chain Monte Carlo methods (MCMC) were used for inference. We propose a new measure of quality for sires, in terms of their posterior probability of being among the, say 10% best sires. The probability is an easily interpretable measure that can be directly used to rank sires. Estimating these complex probabilities is straightforward in an MCMC setting. The results indicate considerable differences between sires with regards to their daughters disease resistance. A regional effect was also discovered with the lowest risk of disease in the south-eastern parts of Norway.     

Critical note on the application of the “two-third” spline

The “two-third spline” (2/3S) is a frequently applied method to detrend tree-ring series. It fits a spline with a 50% frequency cutoff at a frequency equal to two-thirds of each sample length in a dataset. It was introduced to ensure a minimum loss of low-frequency variance, which is resolvable during the detrending of ring-width series.In this paper I show potential problems that arise when rusing this method. The 2/3S runs counter the strengths of using a digital filter to detrend – i.e. one is giving up full control over the frequency-removing characteristics of the growth curve and each individual time series retains a different amount of low frequency. Thus, the 2/3S is less suitable for reconstructing climate or to compare environmental impacts on tree growth between groups – both of which comprise the majority of dendrochronological analyses – as it will likely introduce a temporal frequency bias. Within a long chronology it will result in decreasing power to resolve low frequencies towards present in a living-only trees setting, especially when the youngest segment lengths are 100 years and shorter, and more generally during the period where the chronology is constructed from samples with shorter segment lengths compared to the period with longer segment lengths. The frequency bias will also significantly impact regression slopes and correlation coefficients, possibly distorting analyses investigating multiple groups with different mean segment lengths. Highlighting these potential biases, I recommend the community to not use this method on an individual basis but rather to use a fixed spline stiffness for all samples based on the n% criterion (n = 67) of e.g. the mean segment length of the entire dataset.     

Competition in the gradostat: the role of the communication rate

In this paper we study a mathematical model of competition between two species of microorganisms for a single limiting nutrient in a laboratory device called a gradostat. A gradostat consists of several (we consider only two) chemostats (CSTR's) connected together so that material can flow between the vessels in such a way that a nutrient gradient is established. Our model is a slightly modified version of one considered recently by Jäger et al. [3], in that the rate of exchange of material between the two vessels (the communication rate) is allowed to differ from the dilution rate. The outcome of competition turns out to be surprisingly sensitive to variation of the communication rate. We identify several coexistence regimes in parameter space and describe a method for obtaining operating diagrams for given pairs of competing microorganisms.Research supported in part by NSF Grant DMS 8521605     

Relation between macronuclear DNA and total protein content and generation time in thechilodonella steini (Ciliata) sister cells

Summary Using the monotone dependence function (mdf) together with correlation coefficient it was found that the Ma-DNA content as well as total protein content are regularly, linearly, positively and strongly dependent in sister cells (proter-opisthe) ofChilodonella steini. Additionally it was shown that proter-opisthe ordering is irrelevant to Ma-DNA and protein contents.Analysis of sister cell generation times (TG) confirmed the existence of regular, linear, positive and strong codependence.The relations between Ma-DNA and total protein contents, between protein content and TG, and between Ma-DNA content and TG were also described. There is a weak, linear dependence between Ma-DNA and total protein contents. Relations of TG and Ma-DNA content or TG and total protein content are non-linear and not even monotone. Low and high levels of DNA or proteins are connected with long generation times.     

Quantitative assessment of the accuracy for three interpolation techniques in kinematic analysis of human movement

Marker obstruction during human movement analyses requires interpolation to reconstruct missing kinematic data. This investigation quantifies errors associated with three interpolation techniques and varying interpolated durations. Right ulnar styloid kinematics from 13 participants performing manual wheelchair ramp ascent were reconstructed using linear, cubic spline and local coordinate system (LCS) interpolation from 11–90% of one propulsive cycle. Elbow angles (flexion/extension and pronation/supination) were calculated using real and reconstructed kinematics. Reconstructed kinematics produced maximum elbow flexion/extension errors of 37.1 (linear), 23.4 (spline) and 9.3 (LCS) degrees. Reconstruction errors are unavoidable [minimum errors of 6.7 mm (LCS); 0.29 mm (spline); 0.42 mm (linear)], emphasising careful motion capture system setup must be performed to minimise data interpolation. For the observed movement, LCS-based interpolation (average error of 14.3 mm; correlation of 0.976 for elbow flexion/extension) was most suitable for reconstructing durations longer than 200 ms. Spline interpolation was superior for shorter durations.     

Geometric morphometrics as a tool for interpreting evolutionary transitions in the black fly wing (Diptera: Simuliidae)

A geometric morphometric analysis was conducted on wing‐vein landmarks on exemplar species of the family Simuliidae of the following genera: Parasimulium, Gymnopais, Twinnia, Helodon, Prosimulium, Greniera, Stegopterna, Tlalocomyia, Cnephia, Ectemnia, Metacnephia, Austrosimulium, and Simulium. Generalized least squares superimposition was performed on landmarks, followed by a principal component analysis on resulting Procrustes distances. Patterns of shape change along the principal component axes were visualized using the thin‐plate spline. The analysis revealed wing shape diversity through (1) the insertion points of the subcosta and R₁, resulting in the terminus of the costa exhibiting a trend towards a more apical position on the wing, and (2) the insertion point of the humeral cross vein, resulting in the anterior branch of the media exhibiting a trend toward a more basal position on the wing. Canonical variates analysis of Procrustes distances successfully assigned all exemplar species into their a priori taxonomic groupings. The diversity in wing shape reveals a trend towards decreased length of basal radial cell and increased costalization of anterior wing veins in the evolutionary transition from plesiomorphic prosimuliines to more derived simuliines. The functional significance of these evolutionary transitions is discussed. © 2013 The Linnean Society of London     

Estimation in independent observer line transect surveys for clustered populations

This paper introduces a framework for animal abundance estimation in independent observer line transect surveys of clustered populations. The framework generalizes an approach given in Chen (1999, Environmental and Ecological Statistics 6, in press) to accommodate heterogeneity in detection caused by cluster size and other covariates. Both parametric and nonparametric estimators for the local effective search widths, given the covariates, can be derived from the framework. A nonparametric estimator based on conditional kernel density estimation is proposed and studied owing to its flexibility in modeling the detection functions. A real data set on harbor porpoise in the North Sea is analyzed.     

On the stability of a model of testosterone dynamics

We prove the global asymptotic stability of a well-known delayed negative-feedback model of testosterone dynamics, which has been proposed as a model of oscillatory behavior. We establish stability (and hence the impossibility of oscillations) even in the presence of delays of arbitrary length.Supported in part by AFOSR Grant F49620-01-1-0063, NIH Grant P20 GM64375, and Dimacs.E.D. Sontag: Supported in part by AFOSR Grant F49620-01-1-0063 and NIH Grant R01 GM46383.Acknowledgement We would like to thank Augusto Ponce for useful suggestions.     

Semiparametric estimation of tag loss and reporting rates for tag-recovery experiments using exact time-at-liberty data

We present a semiparametric likelihood approach to estimating reporting rates and tag-loss rates from the tags returned from capture-recapture studies. Such studies are commonly used to estimate critical population parameters. Tag loss rates are estimated using double-tagged animals, while reporting rates are estimated using information from high-reward tags. A likelihood function is constructed based on the conditional distribution of the type of tag returned (low or high reward, single or double tag), given that a tag has been returned. This involves many sparse 5 x 1 tag-return contingency tables, and choosing a good functional form for the tag loss rate is difficult with such data. We model tag-loss rates using monotone-smoothing splines, and use these nonparametric estimates to diagnose the parametric form of the tag-loss rate. The nonparametric methods can also be used directly to model tag-loss rates.