Quantum Dot Interdiffusion For Two Colour Quantum Dot Infrared Photodetectors

An investigation into the effects of thermal interdiffusion on the characteristics of quantum dot infrared photodetectors (QDIPs) yields results useful for the creation of a two-colour QDIP. For high temperature rapid thermal annealing, quantum dot interdiffusion is induced, resulting in a large wavelength redshift in the photodetector spectral response, at the cost of a small degradation in device performance. The evaluation of a two-colour QDIP fabricated using selective suppression of interdiffusion during thermal annealing shows uniform performance in the two different detector pixels. This has implications as a useful process for the future fabrication of multi-colour QDIPs

The atomic waveplate

In this thesis, we theoretically model the behaviour of atoms outcoupled from an atom laser passing through an RF resonance. Within the Landau-Zener formalism, we find a range for the Rabi frequency of the RF field, inside of which dynamical spin transitions occur. We find that atoms exiting the resonance region exhibit symmetric transition into trapped and untrapped spin states. A further numerical model, within the mean field approximation, is performed for an atomic pulse from an atom laser passing through the resonance. The extra coupling between states introduced by the spatial extent of the pulse causes a spread in the momentum of trapped and anti-trapped states that atoms are coupled into within the resonance. An experimental setup for the manipulation of the atomic spin states with an RF field is investigated and designed. The implications of these results is discussed regarding the design of a pumped atom laser using continuous RF evaporation

3D Scanning System for Automatic High-Resolution Plant Phenotyping

Thin leaves, fine stems, self-occlusion, non-rigid and slowly changing structures make plants difficult for three-dimensional (3D) scanning and reconstruction -- two critical steps in automated visual phenotyping. Many current solutions such as laser scanning, structured light, and multiview stereo can struggle to acquire usable 3D models because of limitations in scanning resolution and calibration accuracy. In response, we have developed a fast, low-cost, 3D scanning platform to image plants on a rotating stage with two tilting DSLR cameras centred on the plant. This uses new methods of camera calibration and background removal to achieve high-accuracy 3D reconstruction. We assessed the system's accuracy using a 3D visual hull reconstruction algorithm applied on 2 plastic models of dicotyledonous plants, 2 sorghum plants and 2 wheat plants across different sets of tilt angles. Scan times ranged from 3 minutes (to capture 72 images using 2 tilt angles), to 30 minutes (to capture 360 images using 10 tilt angles). The leaf lengths, widths, areas and perimeters of the plastic models were measured manually and compared to measurements from the scanning system: results were within 3-4% of each other. The 3D reconstructions obtained with the scanning system show excellent geometric agreement with all six plant specimens, even plants with thin leaves and fine stems.Comment: 8 papes, DICTA 201

Interactive and Single Effects of Ectomycorrhiza Formation and Bacillus cereus on Metallothionein MT1 Expression and Phytoextraction of Cd and Zn by Willows

Single and joint ectomycorrhizal (+ Hebeloma mesophaeum) and bacterial (+ Bacillus cereus) inoculations of willows (Salix viminalis) were investigated for their potential and mode of action in the promotion of cadmium (Cd) and zinc (Zn) phytoextraction. Dual fungal and bacterial inoculations promoted the biomass production of willows in contaminated soil. Single inoculations either had no effect on the plant growth or inhibited it. All inoculated willows showed increased concentrations of nutritional elements (N, P, K and Zn) and decreased concentrations of Cd in the shoots. The lowest biomass production and concentration of Cd in the willows (+ B. cereus) were combined with the strongest expression of metallothioneins. It seems that biotic stress from bacterial invasion increased the synthesis of these stress proteins, which responded in decreased Cd concentrations. Contents of Cd and Zn in the stems of willows were combination-specific, but were always increased in dual inoculated plants. In conclusion, single inoculations with former mycorrhiza-associated B. cereus strains decreased the phytoextraction efficiency of willows by causing biotic stress. However, their joint inoculation with an ectomycorrhizal fungus is a very promising method for promoting the phytoextraction of Cd and Zn through combined physiological effects on the plant

Novel Protein-Protein Interactions Inferred from Literature Context

We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature. This method outperforms previously developed PPI prediction algorithms that rely on the conjunction of two protein names in MEDLINE abstracts. We show significant increases in coverage (76% versus 32%) and sensitivity (66% versus 41% at a specificity of 95%) for the prediction of PPIs currently archived in 6 PPI databases. A retrospective analysis shows that PPIs can efficiently be predicted before they enter PPI databases and before their interaction is explicitly described in the literature. The practical value of the method for discovery of novel PPIs is illustrated by the experimental confirmation of the inferred physical interaction between CAPN3 and PARVB, which was based on frequent co-occurrence of both proteins with concepts like Z-disc, dysferlin, and alpha-actinin. The relationships between proteins predicted by our method are broader than PPIs, and include proteins in the same complex or pathway. Dependent on the type of relationships deemed useful, the precision of our method can be as high as 90%. The full set of predicted interactions is available in a downloadable matrix and through the webtool Nermal, which lists the most likely interaction partners for a given protein. Our framework can be used for prioritizing potential interaction partners, hitherto undiscovered, for follow-up studies and to aid the generation of accurate protein interaction maps

Declaration

University. Except where acknowledged in the customary manner, the material presented in this thesis is my own work. ii

Growth Measurement of Arabidopsis in 2.5D from a High Throughput Phenotyping Platform

The last few years have seen an increasing interest in the development of high throughput phenotyping platforms (HTP) that allow the automated measurement of plant growth and structure. These platforms have utilised various imaging technologies, including fluorescence imaging, thermal imaging, and visible imaging. Since plants are structurally complex and inherently three-dimensional (3D), 3D imaging and reconstruction approaches have distinct advantages over 2D imaging when it comes to quantifying structural information (such as leaf angle distribution, leaf area etc.). High throughput phenotyping platforms, when combined with 3D image analysis, enable researchers to investigate complex functional traits related to plant structure, including responses to external and internal signals or perturbations. Moreover, image-based reconstruction techniques are able to produce complex structural models of both large and small individual plants, which retain colour information and are topologically coherent. In this paper, we present a computational workflow for analysing the growth of Arabidopsis thaliana rosettes over time using stereo reconstruction. Stereo reconstruction for plant phenotyping generally includes data collection and point cloud generation. In our approach, we not only use stereo image pairs to generate point clouds of the plants but also reconstruct mesh surfaces for further analysis. By applying a semi-global matching algorithm, 2.5D point clouds of Arabidopsis growing in trays with multiple plants were generated. Point clouds were then filtered and segmented in order to isolate single plants using clustering methods. A variety of surface reconstruction methods were then used to generate meshes from the point clouds. These meshes were analysed to quantify the plant dimensions and surface area in three dimensions. The segmentation was stable over time and was used to generate a time series for the growth of the individual plants over time. The advantages of such a stereo reconstruction system are: i) the system is able to construct realistic point clouds and meshes of the scene, ii) the processing pipeline is computationally efficient, iii) it allows stereo reconstruction and segmentation of individual plants in trays of 20 plants each for high throughput analysis. The overall approach proved useful in quantifying morphometric parameters in 3D for a set of Arabidopsis accessions and relating plant structure to plant function

A Framework for Identifying and Characterising Coral Reef “Oases” against a Backdrop of Degradation

Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances. We developed a framework for identifying oases within coral reef regions using long‐term monitoring data. We calculated standardised estimates of coral cover (z‐scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated “coral calcification capacity” (CCC), a measure of the coral community\u27s ability to produce calcium carbonate structures and tested for an association between this metric and z‐scores of coral cover. We illustrated our z‐score approach within a modelling framework by extracting z‐scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time‐series data from long‐term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo\u27orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z‐scores for median coral cover and were categorised as oases. Synthesis and applications. Our framework provides ecosystem managers with a valuable tool for conservation by identifying “oases” within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z‐scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function