On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies

For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1) in 4 genome-wide association studies

On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies

For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1) in 4 genome-wide association studies

Uniform hypergraphs containing no grids

A hypergraph is called an r×r grid if it is isomorphic to a pattern of r horizontal and r vertical lines, i.e.,a family of sets {A1, ..., Ar, B1, ..., Br} such that Ai∩Aj=Bi∩Bj=φ for 1≤i<j≤r and {pipe}Ai∩Bj{pipe}=1 for 1≤i, j≤r. Three sets C1, C2, C3 form a triangle if they pairwise intersect in three distinct singletons, {pipe}C1∩C2{pipe}={pipe}C2∩C3{pipe}={pipe}C3∩C1{pipe}=1, C1∩C2≠C1∩C3. A hypergraph is linear, if {pipe}E∩F{pipe}≤1 holds for every pair of edges E≠F.In this paper we construct large linear r-hypergraphs which contain no grids. Moreover, a similar construction gives large linear r-hypergraphs which contain neither grids nor triangles. For r≥. 4 our constructions are almost optimal. These investigations are motivated by coding theory: we get new bounds for optimal superimposed codes and designs. © 2013 Elsevier Ltd

Efficient hardware implementations of high throughput SHA-3 candidates keccak, luffa and blue midnight wish for single- and multi-message hashing

In November 2007 NIST announced that it would organize the SHA-3 competition to select a new cryptographic hash function family by 2012. In the selection process, hardware performances of the candidates will play an important role. Our analysis of previously proposed hardware implementations shows that three SHA-3 candidate algorithms can provide superior performance in hardware: Keccak, Luffa and Blue Midnight Wish (BMW). In this paper, we provide efficient and fast hardware implementations of these three algorithms. Considering both single- and multi-message hashing applications with an emphasis on both speed and efficiency, our work presents more comprehensive analysis of their hardware performances by providing different performance figures for different target devices. To our best knowledge, this is the first work that provides a comparative analysis of SHA-3 candidates in multi-message applications. We discover that BMW algorithm can provide much higher throughput than previously reported if used in multi-message hashing. We also show that better utilization of resources can increase speed via different configurations. We implement our designs using Verilog HDL, and map to both ASIC and FPGA devices (Spartan3, Virtex2, and Virtex 4) to give a better comparison with those in the literature. We report total area, maximum frequency, maximum throughput and throughput/area of the designs for all target devices. Given that the selection process for SHA3 is still open; our results will be instrumental to evaluate the hardware performance of the candidates

Evaluation of the 1986-1987 radiata pine clonal trials at Forest Research, New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master in Applied Science at Massey University

Clonal forestry, the establishment of plantations using tested clones, is highly sought after by the forestry industry in New Zealand and worldwide. Clonal testing is a vital element in the process leading to clonal forestry. Two clonal trials established in 1986 and 1987 by the Forest Research Institute with juvenile ortet material have been analysed in this study. The mating design in the 1986 clones-in-family trial was single-pair crossing with amplification of the clones by fascicle cuttings. It was replicated over two sites, and the trait analysed was diameter at 1.40 m height at ages 4,7, and 10 years. The estimation of additive, non-additive and genetic variances showed a high proportion of non-additive variance compared with the additive variance at one of the sites, whereas the proportion was less important at the other site. The high non-additive component of variance can be due to important dominance or epistasis, or to C-effects confounded with the non-additive variance. This trend was similar for all three ages. Realised genetic gains were obtained from selection of clones at age 10 years for clonal deployment and breeding. For clonal deployment, realised gains were high at both sites (13% and 16%). The gains were similar at both sites provided selection was based on performance values at the site, and not on indirect selection on performance of clones at the other site. Realised gains for selection at age 10 based on the performance of clones on combined sites (10% and 13%) were less than the maximum gain obtained at each individual site. Gains based on information from both sites (10% and 12% at respective sites) were more stable than those selections at any one site. For breeding, the level of gain was significantly inferior than for clonal deployment (4% and 8%), especially when the number of clones per family was restricted to one (2% and 4%). Realised gain on combined-site selection yielded less gain than direct selection at the optimum site for selection (1% and 2%). The presence of genotype x environment interaction emphasised the need to test clones in several sites if stability of performance is desired. It is possible to obtain gain from selections made at an early age, but selections made for breeding at the age of final assessment yielded greater expected total gain and gain per unit time. The mating design in the 1987 clones-in-family trial was a 3 x 3 disconnected factorial. The trial was established on a single site and the trait analysed was percentage of Dothistroma needle infection at ages 3,4 and 7years. The mating design allowed estimation of additive, dominance and epistasis variances, which were overestimated for the lack of replication over sites. In this trial measured for Dothistroma resistance, the additive variance was the major component of the genetic variance at both ages. The evolution of components of genetic variance was confounded with the level of Dothistroma infection. The analysis of these trials indicated the need to improve the mating and field designs to improve the accuracy in the estimation of genetic parameters, highlights the importance of annual or biennual measurements to determine trends of those parameters over time, and showed the difference in gains obtained from selection for breeding and clonal deployment for early selection and selection at the age of final assessment. Accuracy in the estimation of genetic parameters can be achieved using factorial mating designs together with serial propagation to reduce the incidence of C effects, and with replication over several sites. Further considerations have to be made to find the most appropriate field and statistical design, but alpha designs are a possibility to explore. Investment in a series of carefully planned clonal trials is fundamental to the future of clonal forestry in radiata pine

Conway Groupoids and Completely Transitive Codes

To each supersimple $2-(n,4,\lambda)$ design \De one associates a `Conway groupoid,' which may be thought of as a natural generalisation of Conway's Mathieu groupoid $M_{13}$ which is constructed from $\mathbb{P}_3$. We show that \Sp_{2m}(2) and 2^{2m}.\Sp_{2m}(2) naturally occur as Conway groupoids associated to certain designs. It is shown that the incidence matrix associated to one of these designs generates a new family of completely transitive $\mathbb{F}_2$-linear codes with minimum distance 4 and covering radius 3, whereas the incidence matrix of the other design gives an alternative construction of a previously known family of completely transitive codes. We also give a new characterization of $M_{13}$ and prove that, for a fixed $\lambda > 0,$ there are finitely many Conway groupoids for which the set of morphisms does not contain all elements of the full alternating group