Prediction of multilocus identity-by-descent

Previous studies have enabled exact prediction of probabilities of identity-by-descent (IBD) in randommating populations for a few loci (up to four or so), with extension to more using approximate regression methods. Here we present a precise predictor of multiple-locus IBD using simple formulas based on exact results for two loci. In particular, the probability of non-IBD X ABC at each of ordered loci A, B, and C can be well approximated by XABC = XABXBC/XB and generalizes to X123. . .k = X12X23. . .Xk-1,k/ Xk-2, where X is the probability of non-IBD at each locus. Predictions from this chain rule are very precise with population bottlenecks and migration, but are rather poorer in the presence of mutation. From these coefficients, the probabilities of multilocus IBD and non-IBD can also be computed for genomic regions as functions of population size, time, and map distances. An approximate but simple recurrence formula is also developed, which generally is less accurate than the chain rule but is more robust with mutation. Used together with the chain rule it leads to explicit equations for non-IBD in a region. The results can be applied to detection of quantitative trait loci (QTL) by computing the probability of IBD at candidate loci in terms of identity-by-state at neighboring markers.

Comment on "Local accumulation times for source, diffusion, and degradation models in two and three dimensions" [J. Chem. Phys. 138, 104121 (2013)]

In a recent paper, Gordon, Muratov, and Shvartsman studied a partial differential equation (PDE) model describing radially symmetric diffusion and degradation in two and three dimensions. They paid particular attention to the local accumulation time (LAT), also known in the literature as the mean action time, which is a spatially dependent timescale that can be used to provide an estimate of the time required for the transient solution to effectively reach steady state. They presented exact results for three-dimensional applications and gave approximate results for the two-dimensional analogue. Here we make two generalizations of Gordon, Muratov, and Shvartsman’s work: (i) we present an exact expression for the LAT in any dimension and (ii) we present an exact expression for the variance of the distribution. The variance provides useful information regarding the spread about the mean that is not captured by the LAT. We conclude by describing further extensions of the model that were not considered by Gordon,Muratov, and Shvartsman. We have found that exact expressions for the LAT can also be derived for these important extensions...

Sparseness vs estimating conditional probabilities : some asymptotic results

One of the nice properties of kernel classifiers such as SVMs is that they often produce sparse solutions. However, the decision functions of these classifiers cannot always be used to estimate the conditional probability of the class label. We investigate the relationship between these two properties and show that these are intimately related: sparseness does not occur when the conditional probabilities can be unambiguously estimated. We consider a family of convex loss functions and derive sharp asymptotic results for the fraction of data that becomes support vectors. This enables us to characterize the exact trade-off between sparseness and the ability to estimate conditional probabilities for these loss functions.

Exact parametric confidence intervals for Bland-Altman limits of agreement

Purpose The previous literature on Bland-Altman analysis only describes approximate methods for calculating confidence intervals for 95% Limits of Agreement (LoAs). This paper describes exact methods for calculating such confidence intervals, based on the assumption that differences in measurement pairs are normally distributed. Methods Two basic situations are considered for calculating LoA confidence intervals: the first where LoAs are considered individually (i.e. using one-sided tolerance factors for a normal distribution); and the second, where LoAs are considered as a pair (i.e. using two-sided tolerance factors for a normal distribution). Equations underlying the calculation of exact confidence limits are briefly outlined. Results To assist in determining confidence intervals for LoAs (considered individually and as a pair) tables of coefficients have been included for degrees of freedom between 1 and 1000. Numerical examples, showing the use of the tables for calculating confidence limits for Bland-Altman LoAs, have been provided. Conclusions Exact confidence intervals for LoAs can differ considerably from Bland and Altman’s approximate method, especially for sample sizes that are not large. There are better, more precise methods for calculating confidence intervals for LoAs than Bland and Altman’s approximate method, although even an approximate calculation of confidence intervals for LoAs is likely to be better than none at all. Reporting confidence limits for LoAs considered as a pair is appropriate for most situations, however there may be circumstances where it is appropriate to report confidence limits for LoAs considered individually.

Foil rolling : a new interpretation of experimental results

This paper explores a new interpretation of experiments on foil rolling. The assumption that the roll remains convex is relaxed so that the strip profile may become concave, or thicken in the roll gap. However, we conjecture that the concave profile is associated with phenomena which occur after the rolls have stopped. We argue that the yield criterion must be satisfied in a nonconventional manner if such a phenomenon is caused plastically. Finite element analysis on an extrusion problem appears to confirm this conjecture.

An innovative learning model for teaching architectural technology using building information modelling : a Queensland University of Technology perspective

In architecture courses, instilling a wider understanding of the industry specific representations practiced in the Building Industry is normally done under the auspices of Technology and Science subjects. Traditionally, building industry professionals communicated their design intentions using industry specific representations. Originally these mainly two dimensional representations such as plans, sections, elevations, schedules, etc. were produced manually, using a drawing board. Currently, this manual process has been digitised in the form of Computer Aided Design and Drafting (CADD) or ubiquitously simply CAD. While CAD has significant productivity and accuracy advantages over the earlier manual method, it still only produces industry specific representations of the design intent. Essentially, CAD is a digital version of the drawing board. The tool used for the production of these representations in industry is still mainly CAD. This is also the approach taken in most traditional university courses and mirrors the reality of the situation in the building industry. A successor to CAD, in the form of Building Information Modelling (BIM), is presently evolving in the Construction Industry. CAD is mostly a technical tool that conforms to existing industry practices. BIM on the other hand is revolutionary both as a technical tool and as an industry practice. Rather than producing representations of design intent, BIM produces an exact Virtual Prototype of any building that in an ideal situation is centrally stored and freely exchanged between the project team. Essentially, BIM builds any building twice: once in the virtual world, where any faults are resolved, and finally, in the real world. There is, however, no established model for learning through the use of this technology in Architecture courses. Queensland University of Technology (QUT), a tertiary institution that maintains close links with industry, recognises the importance of equipping their graduates with skills that are relevant to industry. BIM skills are currently in increasing demand throughout the construction industry through the evolution of construction industry practices. As such, during the second half of 2008, QUT 4th year architectural students were formally introduced for the first time to BIM, as both a technology and as an industry practice. This paper will outline the teaching team’s experiences and methodologies in offering a BIM unit (Architectural Technology and Science IV) at QUT for the first time and provide a description of the learning model. The paper will present the results of a survey on the learners’ perspectives of both BIM and their learning experiences as they learn about and through this technology.

Final report: stage 1 : results

This research project aims to improve economic, social and environmental sustainability of the pre-cast concrete and construction and demolition waste supply chains through the development, trial and evaluation of an innovative supply chain management strategy. The long-term goals are to improve competitive behaviour and market sector performance and improve business process efficiency and effectiveness of public sector program delivery by influencing policy development, changing organisational behaviour and implementation development to achieve more economic, social and environmental sustainable markets.

Development of a biaxial compression device for biological samples : preliminary experimental results for a closed cell foam

Biological tissues are subjected to complex loading states in vivo and in order to define constitutive equations that effectively simulate their mechanical behaviour under these loads, it is necessary to obtain data on the tissue's response to multiaxial loading. Single axis and shear testing of biological tissues is often carried out, but biaxial testing is less common. We sought to design and commission a biaxial compression testing device, capable of obtaining repeatable data for biological samples. The apparatus comprised a sealed stainless steel pressure vessel specifically designed such that a state of hydrostatic compression could be created on the test specimen while simultaneously unloading the sample along one axis with an equilibrating tensile pressure. Thus a state of equibiaxial compression was created perpendicular to the long axis of a rectangular sample. For the purpose of calibration and commissioning of the vessel, rectangular samples of closed cell ethylene vinyl acetate (EVA) foam were tested. Each sample was subjected to repeated loading, and nine separate biaxial experiments were carried out to a maximum pressure of 204 kPa (30 psi), with a relaxation time of two hours between them. Calibration testing demonstrated the force applied to the samples had a maximum error of 0.026 N (0.423% of maximum applied force). Under repeated loading, the foam sample demonstrated lower stiffness during the first load cycle. Following this cycle, an increased stiffness, repeatable response was observed with successive loading. While the experimental protocol was developed for EVA foam, preliminary results on this material suggest that this device may be capable of providing test data for biological tissue samples. The load response of the foam was characteristic of closed cell foams, with consolidation during the early loading cycles, then a repeatable load-displacement response upon repeated loading. The repeatability of the test results demonstrated the ability of the test device to provide reproducible test data and the low experimental error in the force demonstrated the reliability of the test data.

Expression of Potato virus Y cytoplasmic inclusion protein in tobacco results in disorganization of parenchyma cells, distortion of epidermal cells, and induces mitochondrial and chloroplast abnormalities, formation of membrane whorls and atypical lipid accumulation

Infection of plant cells by potyviruses induces the formation of cytoplasmic inclusions ranging in size from 200 to 1000 nm. To determine if the ability to form these ordered, insoluble structures is intrinsic to the potyviral cytoplasmic inclusion protein, we have expressed the cytoplasmic inclusion protein from Potato virus Y in tobacco under the control of the chrysanthemum ribulose-1,5-bisphosphate carboxylase small subunit promoter, a highly active, green tissue promoter. No cytoplasmic inclusions were observed in the leaves of transgenic tobacco using transmission electron microscopy, despite being able to clearly visualize these inclusions in Potato virus Y infected tobacco leaves under the same conditions. However, we did observe a wide range of tissue and sub-cellular abnormalities associated with the expression of the Potato virus Y cytoplasmic inclusion protein. These changes included the disruption of normal cell morphology and organization in leaves, mitochondrial and chloroplast internal reorganization, and the formation of atypical lipid accumulations. Despite these significant structural changes, however, transgenic tobacco plants were viable and the results are discussed in the context of potyviral cytoplasmic inclusion protein function.

How to extract and expand randomness : a summary and explanation of existing results

We examine the use of randomness extraction and expansion in key agreement (KA) pro- tocols to generate uniformly random keys in the standard model. Although existing works provide the basic theorems necessary, they lack details or examples of appropriate cryptographic primitives and/or parameter sizes. This has lead to the large amount of min-entropy needed in the (non-uniform) shared secret being overlooked in proposals and efficiency comparisons of KA protocols. We therefore summa- rize existing work in the area and examine the security levels achieved with the use of various extractors and expanders for particular parameter sizes. The tables presented herein show that the shared secret needs a min-entropy of at least 292 bits (and even more with more realistic assumptions) to achieve an overall security level of 80 bits using the extractors and expanders we consider. The tables may be used to �nd the min-entropy required for various security levels and assumptions. We also �nd that when using the short exponent theorems of Gennaro et al., the short exponents may need to be much longer than they suggested.

Collaboration using BIM : results of cooperative research centre for construction innovation projects

This paper discusses the issues with sharing information between different disciplines in collaborative projects. The focus is on the information itself rather than the wider issues of collaboration. A range of projects carried out by the Cooperative Research Centre for Construction Innovation (CRC CI) in Australia is used to illustrate the issues.