Variation in actual relationship among descendants of inbred individuals

In previous analyses, the variation in actual, or realized, relationship has been derived as a function of map length of chromosomes and type of relationship, the variation being greater the shorter the total chromosome length and the coefficient of variation being greater the more distant the relationship. Here, the results are extended to allow for the relatives' ancestor being inbred. Inbreeding of a parent reduces variation in actual relationship among its offspring, by an amount that depends on the inbreeding level and the type of mating that led to that level. For descendants of full-sibs, the variation is reduced in later generations, but for descendants of half-sibs, it is increased

Fluxoid formation: size effects and non-equilibrium universality

Simple causal arguments put forward by Kibble and Zurek suggest that the scaling behaviour of condensed matter at continuous transitions is related to the familiar universality classes of the systems at quasi-equilibrium. Although proposed 25 years ago or more, it is only in the last few years that it has been possible to devise experiments from which scaling exponents can be determined and in which this scenario can be tested. In previous work, an unusually high Kibble-Zurek scaling exponent was reported for spontaneous fluxoid production in a single isolated superconducting Nb loop, albeit with low density. Using analytic approximations backed up by Langevin simulations, we argue that densities as small as these are too low to be attributable to scaling, and are conditioned by the small size of the loop. We also reflect on the physical differences between slow quenches and small rings, and derive some criteria for these differences, noting that recent work on slow quenches does not adequately explain the anomalous behaviour seen here.Comment: 7 pages, 4 figures, presentation given at CMMP 201

Fractal Characterizations of MAX Statistical Distribution in Genetic Association Studies

Two non-integer parameters are defined for MAX statistics, which are maxima of $d$ simpler test statistics. The first parameter, $d_{MAX}$, is the fractional number of tests, representing the equivalent numbers of independent tests in MAX. If the $d$ tests are dependent, $d_{MAX} < d$. The second parameter is the fractional degrees of freedom $k$ of the chi-square distribution $\chi^2_k$ that fits the MAX null distribution. These two parameters, $d_{MAX}$ and $k$, can be independently defined, and $k$ can be non-integer even if $d_{MAX}$ is an integer. We illustrate these two parameters using the example of MAX2 and MAX3 statistics in genetic case-control studies. We speculate that $k$ is related to the amount of ambiguity of the model inferred by the test. In the case-control genetic association, tests with low $k$ (e.g. $k=1$) are able to provide definitive information about the disease model, as versus tests with high $k$ (e.g. $k=2$) that are completely uncertain about the disease model. Similar to Heisenberg's uncertain principle, the ability to infer disease model and the ability to detect significant association may not be simultaneously optimized, and $k$ seems to measure the level of their balance

Highly syntenic and yet divergent: a tale of two Theilerias

The published genomic sequences of the two major host-transforming Theileria species of cattle represent a rich resource of information that has allowed novel bioinformatic and experimental studies into these important apicomplexan parasites. Since their publication in 2005, the genomes of T. annulata and T. parva have been utilised for a diverse range of applications, ranging from candidate antigen discovery to the identification of genetic markers for population analysis. This has led to advancements in the quest for a sub-unit vaccine, while providing a greater understanding of variation among parasite populations in the field. The unique ability of these Theileria species to induce host cell transformation is the subject of considerable scientific interest and the availability of full genomic sequences has provided new insights into this area of research. This article reviews the data underlying published comparative analyses, focussing on the general features of gene expression, the major Tpr/Tar multi-copy gene family and a re-examination of the predicted macroschizont secretome. Codon usage between the Theileria species is reviewed in detail, as this underpins ongoing comparative studies investigating selection at the intra- and inter-species level. The TashAT/TpshAT family of genes, conserved between T. annulata and T. parva, encodes products targeted to the host nucleus and has been implicated in contributing to the transformed bovine phenotype. Species-specific expansion and diversification at this critical locus is discussed with reference to the availability, in the near future, of genomic datasets which are based on non-transforming Theileria species

Variation in actual relationship as a consequence of Mendelian sampling and linkage

Although the expected relationship or proportion of genome shared by pairs of relatives can be obtained from their pedigrees, the actual quantities deviate as a consequence of Mendelian sampling and depend on the number of chromosomes and map length. Formulae have been published previously for the variance of actual relationship for a number of specific types of relatives but no general formula for non-inbred individuals is available. We provide here a unified framework that enables the variances for distant relatives to be easily computed, showing, for example, how the variance of sharing for great grandparent–great grandchild, great uncle–great nephew, half uncle–nephew and first cousins differ, even though they have the same expected relationship. Results are extended in order to include differences in map length between sexes, no recombination in males and sex linkage. We derive the magnitude of skew in the proportion shared, showing the skew becomes increasingly large the more distant the relationship. The results obtained for variation in actual relationship apply directly to the variation in actual inbreeding as both are functions of genomic coancestry, and we show how to partition the variation in actual inbreeding between and within families. Although the variance of actual relationship falls as individuals become more distant, its coefficient of variation rises, and so, exacerbated by the skewness, it becomes increasingly difficult to distinguish different pedigree relationships from the actual fraction of the genome shared

Determination of Effective Permittivity and Permeability of Metamaterials from Reflection and Transmission Coefficients

We analyze the reflection and transmission coefficients calculated from transfer matrix simulations on finite lenghts of electromagnetic metamaterials, to determine the effective permittivity and permeability. We perform this analysis on structures composed of periodic arrangements of wires, split ring resonators (SRRs) and both wires and SRRs. We find the recovered frequency-dependent permittivity and permeability are entirely consistent with analytic expressions predicted by effective medium arguments. Of particular relevance are that a wire medium exhibits a frequency region in which the real part of permittivity is negative, and SRRs produce a frequency region in which the real part of permeability is negative. In the combination structure, at frequencies where both the recovered real part of permittivity and permeability are simultaneously negative, the real part of the index-of-refraction is found also to be unambigously negative.Comment: *.pdf file, 5 figure

Laser microdrilling in the fabrication of laser fusion targets

A brief discussion on the use and performance of laser microdrilling is given. The fabrication of a ''ball-in-plate'' fusion target is described. (MOW