Visual analytics for large-scale bioinformatic data sets

Rapid advances in sequencing technologies (Next Generation Sequencing or NGS) have led to a vast increase in the quantity of bioinformatics data available, with this increasing scale presenting enormous challenges to researchers seeking to identify complex interactions. This paper is concerned with the domain of transcriptional regulation, and the use of visualisation to identify relationships between specific regulatory proteins (the transcription factors or TFs) and their associated target genes (TGs). We present preliminary work from an ongoing study which aims to determine the effectiveness of different visual representations and large scale displays in supporting discovery. Following an iterative process of implementation and evaluation, representations were tested by potential users in the bioinformatics domain to determine their efficacy, and to understand better the range of ad hoc practices among bioinformatics literate users. Results from two rounds of small scale user studies are considered with initial findings suggesting that bioinformaticians require richly detailed views of TF data, features to compare TF layouts between organisms quickly, and ways to keep track of interesting data points.

Efficient designs for sampling and subsampling in fisheries research based on ranked sets

Sampling strategies are developed based on the idea of ranked set sampling (RSS) to increase efficiency and therefore to reduce the cost of sampling in fishery research. The RSS incorporates information on concomitant variables that are correlated with the variable of interest in the selection of samples. For example, estimating a monitoring survey abundance index would be more efficient if the sampling sites were selected based on the information from previous surveys or catch rates of the fishery. We use two practical fishery examples to demonstrate the approach: site selection for a fishery-independent monitoring survey in the Australian northern prawn fishery (NPF) and fish age prediction by simple linear regression modelling a short-lived tropical clupeoid. The relative efficiencies of the new designs were derived analytically and compared with the traditional simple random sampling (SRS). Optimal sampling schemes were measured by different optimality criteria. For the NPF monitoring survey, the efficiency in terms of variance or mean squared errors of the estimated mean abundance index ranged from 114 to 199% compared with the SRS. In the case of a fish ageing study for Tenualosa ilisha in Bangladesh, the efficiency of age prediction from fish body weight reached 140%.

Flow of metal into the flash gap in the last stages of a plane-strain closed-die forging operation

In closed-die forging the flash geometry should be such as to ensure that the cavity is completely filled just as the two dies come into contact at the parting plane. If metal is caused to extrude through the flash gap as the dies approach the point of contact — a practice generally resorted to as a means of ensuring complete filling — dies are unnecessarily stressed in a high-stress regime (as the flash is quite thin and possibly cooled by then), which reduces the die life and unnecessarily increases the energy requirement of the operation. It is therefore necessary to carefully determine the dimensions of the flash land and flash thickness — the two parameters, apart from friction at the land, which control the lateral flow. The dimensions should be such that the flow into the longitudinal cavity is controlled throughout the operation, ensuring complete filling just as the dies touch at the parting plane. The design of the flash must be related to the shape and size of the forging cavity as the control of flow has to be exercised throughout the operation: it is possible to do this if the mechanics of how the lateral extrusion into the flash takes place is understood for specific cavity shapes and sizes. The work reported here is part of an ongoing programme investigating flow in closed-die forging. A simple closed shape (no longitudinal flow) which may correspond to the last stages of a real forging operation is analysed using the stress equilibrium approach. Metal from the cavity (flange) flows into the flash by shearing in the cavity in one of the three modes considered here: for a given cavity the mode with the least energy requirement is assumed to be the most realistic. On this basis a map has been developed which, given the depth and width of the cavity as well as the flash thickness, will tell the designer of the most likely mode (of the three modes considered) in which metal in the cavity will shear and then flow into the flash gap. The results of limited set of experiments, reported herein, validate this method of selecting the optimum model of flow into the flash gap.

Closed-form solutions for low-rank non-rigid reconstruction

Recovering the motion of a non-rigid body from a set of monocular images permits the analysis of dynamic scenes in uncontrolled environments. However, the extension of factorisation algorithms for rigid structure from motion to the low-rank non-rigid case has proved challenging. This stems from the comparatively hard problem of finding a linear “corrective transform” which recovers the projection and structure matrices from an ambiguous factorisation. We elucidate that this greater difficulty is due to the need to find multiple solutions to a non-trivial problem, casting a number of previous approaches as alleviating this issue by either a) introducing constraints on the basis, making the problems nonidentical, or b) incorporating heuristics to encourage a diverse set of solutions, making the problems inter-dependent. While it has previously been recognised that finding a single solution to this problem is sufficient to estimate cameras, we show that it is possible to bootstrap this partial solution to find the complete transform in closed-form. However, we acknowledge that our method minimises an algebraic error and is thus inherently sensitive to deviation from the low-rank model. We compare our closed-form solution for non-rigid structure with known cameras to the closed-form solution of Dai et al. [1], which we find to produce only coplanar reconstructions. We therefore make the recommendation that 3D reconstruction error always be measured relative to a trivial reconstruction such as a planar one.

Approximate closed-form solutions of realistic true proportional navigation guidance using the Adomian decomposition method

Approximate closed-form solutions of the non-linear relative equations of motion of an interceptor pursuing a target under the realistic true proportional navigation (RTPN) guidance law are derived using the Adomian decomposition method in this article. In the literature, no study has been reported on derivation of explicit time-series solutions in closed form of the nonlinear dynamic engagement equations under the RTPN guidance. The Adomian method provides an analytical approximation, requiring no linearization or direct integration of the non-linear terms. The complete derivation of the Adomian polynomials for the analysis of the dynamics of engagement under RTPN guidance is presented for deterministic ideal case, and non-ideal dynamics in the loop that comprises autopilot and actuator dynamics and target manoeuvre, as well as, for a stochastic case. Numerical results illustrate the applicability of the method.

A comparison of plotless density estimators using Monte Carlo simulation on totally enumerated field data sets

Background: Plotless density estimators are those that are based on distance measures rather than counts per unit area (quadrats or plots) to estimate the density of some usually stationary event, e.g. burrow openings, damage to plant stems, etc. These estimators typically use distance measures between events and from random points to events to derive an estimate of density. The error and bias of these estimators for the various spatial patterns found in nature have been examined using simulated populations only. In this study we investigated eight plotless density estimators to determine which were robust across a wide range of data sets from fully mapped field sites. They covered a wide range of situations including animal damage to rice and corn, nest locations, active rodent burrows and distribution of plants. Monte Carlo simulations were applied to sample the data sets, and in all cases the error of the estimate (measured as relative root mean square error) was reduced with increasing sample size. The method of calculation and ease of use in the field were also used to judge the usefulness of the estimator. Estimators were evaluated in their original published forms, although the variable area transect (VAT) and ordered distance methods have been the subjects of optimization studies. Results: An estimator that was a compound of three basic distance estimators was found to be robust across all spatial patterns for sample sizes of 25 or greater. The same field methodology can be used either with the basic distance formula or the formula used with the Kendall-Moran estimator in which case a reduction in error may be gained for sample sizes less than 25, however, there is no improvement for larger sample sizes. The variable area transect (VAT) method performed moderately well, is easy to use in the field, and its calculations easy to undertake. Conclusion: Plotless density estimators can provide an estimate of density in situations where it would not be practical to layout a plot or quadrat and can in many cases reduce the workload in the field.

Closed Systems

Closed Systems was an exhibition of sculptural works held at MetroArts, Brisbane in the group exhibition 'Platform 2012' curated by Jan Manton. My contribution to the group show was a series of 13 bronze sculptures, produced using a lost-wax casting process. Each form was derived from a sapling that had been manipulated so that branches and roots were interconnected. The resulting 'looped' forms evoked notions on narcissism, self-absorption and introversion. The works were subsequently exhibited at the National Arts School in Sydney as part of the Kodak Minolta Art Prize (2013).

A Closed-Cycle Refrigerator Based Pulsed Management System

A low cost 12 T pulsed magnet system has been integrated with a closed-cycle helium refrigerator. The copper solenoid is directly immersed in liquid nitrogen for reduced electrical resistance and more efficient heat transfer. This ensures a minimal delay of few minutes between pulses. The sample is mounted on the cold finger of the refrigerator and, along with the surrounding vacuum shroud, is inserted into the bore of the solenoid. When combined with software lock-in signal processing to reduce noise, quick but accurate measurements can be performed at temperatures 4 K-300 K up to 12 T. Quantum Hall effect data in a p-channel SiGe/Si heterostructure has been used to calibrate the instrument against a commercial superconducting magnet. Its versatility as a routine characterization tool is demonstrated bymeasuring parallel conduction in Si/SiGe modulation doped heterostructures.

X-ray studies on crystalline complexes involving amino acids and peptides. Part XIV: Closed conformation and head-to-tail arrangement in a new crystal form of L-histidine L-aspartate monohydrate

A new form of L-histidine L-aspartate monohydrate crystallizes in space group P22 witha = 5.131(1),b = 6.881(1),c= 18.277(2) Å,β= 97.26(1)° and Z = 2. The structure has been solved by the direct methods and refined to anR value of 0.044 for 1377 observed reflections. Both the amino acid molecules in the complex assume the energetically least favourable allowed conformation with the side chains staggered between the α-amino and α-scarboxylate groups. This results in characteristic distortions in some bond angles. The unlike molecules aggregate into alternating double layers with water molecules sandwiched between the two layers in the aspartate double layer. The molecules in each layer are arranged in a head-to-tail fashion. The aggregation pattern in the complex is fundamentally similar to that in other binary complexes involving commonly occurring L amino acids, although the molecules aggregate into single layers in them. The distribution of crystallographic (and local) symmetry elements in the old form of the complex is very different from that in the new form. So is the conformation of half the histidine molecules. Yet, the basic features of molecular aggregation, particularly the nature and the orientation of head-to-tail sequences, remain the same in both the forms. This supports the thesis that the characteristic aggregation patterns observed in crystal structures represent an intrinsic property of amino acid aggregation.

Micro-CT based characterisation of changes to the vascular network following closed soft tissue trauma and cryotherapy

This project has investigated how the architecture of the blood vessels supplying nutrients to skeletal muscles is affected by muscle contusion injuries, and how it changes during healing with or without initial treatment of the injury by icing. In order to do this, we used contrast agents to visualise blood vessels in 3D with micro-computed tomography imaging. This research significantly contributes to the fields of orthopaedics, traumatology and sports medicine, as it improves our understanding of muscle contusion injuries. Furthermore, the methods developed in this thesis may help to improve the diagnosis and monitoring of these injuries.

Estimation Of Properties Of Rare-Gas Solids From Compression Characteristics Of Closed-Shell Ions

We present a unified approach to repulsion in ionic and van der Waals solids based on a compressible-ion/atom model. Earlier studies have shown that repulsion in ionic crystals can be viewed as arising from the compression energy of ions, described by two parameters per ion. Here we obtain the compression parameters of the rare-gas atoms Ne. Ar. Kr and Xe by interpolation using the known parameters of related equi-electronic ions (e.g. Ar from S2-. Cl-, K- and Ca2-). These parameters fit the experimental zero-temperature interatomic distances and compressibilities of the rare-gas crystals satisfactorily. A hightemperature equation of state based on an Einstein model of thermal motions is used to calculate the thermal expansivities, compressibilities and their temperature derivatives for Ar. Kr and Xe. It is argued that an instability at higher temperatures represents the limit to which the solid can be superheated. beyond which sublimation must occur.

Reliable Means of Diagnosis and Serovar Determination of Blood-Borne Salmonella Strains: Quick PCR Amplification of Unique Genomic Loci by Novel Primer Sets

Typhoid fever is becoming an ever increasing threat in the developing countries. We have improved considerably upon the existing PCR-based diagnosis method by designing primers against a region that is unique to Salmonella enterica subsp. enterica serovar Typhi and Salmonella enterica subsp. enterica serovar Paratyphi A, corresponding to the STY0312 gene in S. Typhi and its homolog SPA2476 in S. Paratyphi A. An additional set of primers amplify another region in S. Typhi CT18 and S. Typhi Ty2 corresponding to the region between genes STY0313 to STY0316 but which is absent in S. Paratyphi A. The possibility of a false-negative result arising due to mutation in hypervariable genes has been reduced by targeting a gene unique to typhoidal Salmonella serovars as a diagnostic marker. The amplified region has been tested for genomic stability by amplifying the region from clinical isolates of patients from various geographical locations in India, thereby showing that this region is potentially stable. These set of primers can also differentiate between S. Typhi CT18, S. Typhi Ty2, and S. Paratyphi A, which have stable deletions in this specific locus. The PCR assay designed in this study has a sensitivity of 95% compared to the Widal test which has a sensitivity of only 63%. As observed, in certain cases, the PCR assay was more sensitive than the blood culture test was, as the PCR-based detection could also detect dead bacteria.

A Branch and Bound Algorithm for a Transportation Type Problem with Piecewise Linear Convex Objective Function

A branch and bound type algorithm is presented in this paper to the problem of finding a transportation schedule which minimises the total transportation cost, where the transportation cost over each route is assumed to be a piecewice linear continuous convex function with increasing slopes. The algorithm is an extension of the work done by Balachandran and Perry, in which the transportation cost over each route is assumed to beapiecewise linear discontinuous function with decreasing slopes. A numerical example is solved illustrating the algorithm.

Boundedness and convergence of singular integrals on fractal type sets

The topic of this dissertation lies in the intersection of harmonic analysis and fractal geometry. We particulary consider singular integrals in Euclidean spaces with respect to general measures, and we study how the geometric structure of the measures affects certain analytic properties of the operators. The thesis consists of three research articles and an overview. In the first article we construct singular integral operators on lower dimensional Sierpinski gaskets associated with homogeneous Calderón-Zygmund kernels. While these operators are bounded their principal values fail to exist almost everywhere. Conformal iterated function systems generate a broad range of fractal sets. In the second article we prove that many of these limit sets are porous in a very strong sense, by showing that they contain holes spread in every direction. In the following we connect these results with singular integrals. We exploit the fractal structure of these limit sets, in order to establish that singular integrals associated with very general kernels converge weakly. Boundedness questions consist a central topic of investigation in the theory of singular integrals. In the third article we study singular integrals of different measures. We prove a very general boundedness result in the case where the two underlying measures are separated by a Lipshitz graph. As a consequence we show that a certain weak convergence holds for a large class of singular integrals.