Science

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  • (2022) Nguyen, Robert
    Thesis
    Data-driven decision making is everywhere in the modern sporting world. The most well-known example of this is the Moneyball movement in Major League Baseball (MLB), which built on research by Sherri Nichols in the 1980s, but sport analytics has also driven major changes in strategy in basketball, the National Football League, and soccer. In Australia, sports analytics has not had quite the same influence in its major domestic codes. In this thesis, we develop tools to assist the analytics community in two major Australian commercial sports. For Australian Rules Football, the largest commercial sport in Australia, data was not readily accessible for the national competition, the Australian Football League (AFL). Data access is fundamental to data analysis, so this has been a major constraint on the capacity of the AFL analytics community to grow. In this thesis, this issued is solved by making AFL data readily accessible through the R package fitzRoy. This package has already proven to be quite successful and has seen uptake from the media, fans, and club analysts. Expected points models are widely used across sports to inform tactical decision making, but as currently implemented, they confound the effects of decisions on points scored and the situations that the decisions tend to be made in. In Chapter 3, a new expected points approach is proposed, which conditions on match situation when estimating the effect of decisions on expected points. Hence we call this a conditional Expected Points (cEP) model. Our cEP model is used to provide new insight into fourth Down (NFL) decision-making in the National Football League, and decision-making when awarded a penalty in Rugby League. The National Rugby League (NRL) is the leading competition of Australia’s second largest commercial sport it is played on a pitch that is 100m long and 70m wide, and the NRL have provided us with detailed event data from the previous five seasons, used in academic research for the first time in this thesis. We found that NRL teams should kick for goal from penalties much more often than is currently the case. In Chapter 4 we develop a live probability model for predicting the winner of a Rugby League game using data that is collected live. This model could be used by the National Rugby League during broadcasts to enhance their coverage by reporting live win probabilities. While most live probability models are constructed using scores only, the availability of live event data meant we could investigate whether models constructed using event data have better predictive performance. We were able to show that in addition to score differential that the addition of covariates such as missed tackles can improve the prediction. Clubs use their own domain knowledge to test their own live win probability theories with the R scripts that are provided to the NRL

  • (2022) Gautam, Shreedhar
    Thesis
    Extracellular vesicles (EVs) are phospholipid membrane bound sacs (vesicles) produced from almost all types of cells. They are found in circulation and contain the cargo biomolecules such as nucleic acids, proteins, lipids, and amino acids. EVs are involved in trafficking these biomolecules between cells and as such have the role in physiological and pathological processes. EVs are heterogenous and revealing their heterogeneity is crucial to understand their explicit physiological and pathological roles. Current isolation techniques cannot sort EVs based on their biogenesis and provides average information instead of each EVs subtype. Thus, single EVs analysis was popular and many surface protein characterization techniques are developed. But there are no techniques available for internal cargo analysis of individual EVs. The overall aim was to develop a technique to analyse internal microRNA cargo content, if possible, for single EVs, if not from the minimum number of EVs. To achieve that goal, light activated electrochemistry, a technique where focused light beam was illuminated on the semiconductor surface and make it electrochemically active was used. The surface was protected against oxidation during electrochemical reactions by grafting self-assembled monolayer of 1,8-nonadiyne. Then, silicon-based surface was patterned with polymers, antibodies, and cells using the light patterns. As a result, the first milestone to prepare light-assisted patterned semiconductor surface was achieved for our overall aim of analysing content of individual EVs. The size range of EVs is 30 to 200 nm, still very low compared to 30 µm which is the best spatial resolution achieved for light activated electrochemistry using crystalline silicon. Thus, chapter 4 developed a technique to improve the spatial resolution of light activated electrochemistry using amorphous silicon. Amorphous silicon has short diffusion length of charge carriers compared to crystalline silicon due to the defect states in band gap called as localized states. So, charge carriers are frequently trapped in these localized states leading to 60 times improvement in spatial resolution to 500 nm. But even this spatial resolution was not enough to analyse individual EVs. So, microRNA content from pool of EVs were detected using the screen-printed electrodes in a high throughput manner instead of single EVs.

  • (2022) Cao, Jun
    Thesis
    This thesis focuses on the development and applications of magnetic resonance electrical properties tomography (MREPT), which is an emerging imaging modality to noninvasively obtain the electrical properties of tissues, such as conductivity and permittivity. Chapter 2 describes the general information about human research ethics, MRI scanner, MR sequence and the method of phase-based MREPT implemented in this thesis. Chapter 3 examines the repeatability of phase-based MREPT in the brain conductivity measurement using balanced fast field echo (bFFE) and turbo spin echo (TSE) sequences, and investigate the effects of compressed SENSE, whole-head B_1 shimming and video watching during scan on the measurement precision. Chapter 4 investigates the conductivity signal in response to short-duration visual stimulus, compares the signal and functional activation pathway with that of BOLD, and tests the consistency of functional conductivity imaging (funCI) with visual stimulation across participants. Chapter 5 extends the use of functional conductivity imaging to somatosensory stimulation and trigeminal nerve stimulation to evaluate the consistency of functional conductivity activation across different types of stimuli. In addition, visual adaptation experiment is performed to test if the repetition suppression effect can be observed using funCI. Chapter 6 explores if resting state conductivity networks can be reliably constructed using resting state funCI, evaluates the consistency of persistent homology architectures, and compares the links between nodes in the whole brain. Chapter 7 investigates the feasibility of prostate conductivity imaging using MREPT, and distinctive features in the conductivity distribution between healthy participants and participants with suspected abnormalities.

  • (2022) Wang, Shuangyue
    Thesis
    Two-dimensional transition metal dichalcogenide (TMD) nanocrystals (NCs) exhibit unique optical and electrocatalytic properties. However, the growth of uniform and high-quality NCs of monolayer TMD remains a challenge. Until now, most of them are synthesized via solution-based hydrothermal process or ultrasonic exfoliation method, in which the capping ligands introduced from organic solution often quench the optical and electrocatalytic properties of TMD NCs. Moreover, it is difficult to homogeneously disperse the solution-based TMD NCs on a substrate for device fabrication since the dispersed NCs can easily aggregate. Here, we put forward a novel CVD method to grow closely-spaced TMD NCs and explored the growth mechanism and attempts on the size control. Their applications acting as electrocatalysts and adhesion layer for Au film deposition have been also well displayed. Through the whole chapters of this thesis, the following aspects are highlighted: 1. MoS2 and other TMD nanocrystals have been grown on the c-plane sapphire. The surface oxygen vacancies determine the density of TMD nanocrystals. The MoS2 nanocrystals demonstrate excellent hydrogen evolution reaction and surface-enhanced Raman scattering performance owing to the abundant edges. 2. Deep insights into the growth of MoS2 nanograins have been explored. The surface step edges and lattice structures of the underlying sapphire substrates have a significant influence on the growth behaviors. The step edges could modulate the aggregation of MoS2 nanograins to form unidirectional triangular islands. The Raman spectra of MoS2 demonstrate a linear relationship with the crystal size of MoS2. 3. The orientation of sapphire substrate has an of importance effect on the critical size of MoS2 nanocrystals. The MoS2 nanocrystals have the smallest size on the r-plane sapphire, besides, the MoS2 on r-plane sapphire demonstrates the sintering-resistance feature, which is attributed to the edge-pinning effect when MoS2 edges are anchored on the sapphire surface. 4. The MoS2 nanocrystalline layer was utilized as the adhesion layer for Au film depositing on a sapphire substrate. The Au films on MoS2 displayed superior transmittance and electrical conductivity as well as outstanding thermal stability, which lay in the strong binding of Au film with MoS2 nanocrystalline layer.

  • (2022) Bartolec-Criss, Tara
    Thesis
    The function of a protein is mediated by its ability to form precise three-dimensional structures or specific protein-protein interaction (PPI) interfaces. However, it has been challenging to study these aspects of the proteome at scale, in sufficient detail, and in a generalisable way. Cross-linking mass spectrometry (XL-MS) performed on high complexity samples (such as entire organelles or cells) theoretically enables the large scale mapping and monitoring of protein structural conformations and PPI interfaces in native proteoforms. However, as the large scale XL-MS field is young and historically driven by the reporting of technological innovations, assessment of the biological accuracy (and overall utility) of large scale XL-MS studies is still largely underexplored. This thesis applies large scale XL-MS to two eukaryotic systems (Saccharomyces cerevisiae and cultured human cells) and is presented as three independent studies. Firstly, it reports the first budding yeast XL-MS interactome, generated by cross-linking intact nuclei isolated from wild-type cells with DSSO. The wealth of yeast interactome data enabled identification of an inflated false discovery rate for cross-links representing PPIs, and development of a novel quality control approach. Surprisingly, the high confidence PPIs were substantially orthogonal to historical binary interactome mapping efforts. Subsequently, it reports the largest XL-MS dataset currently available for any species, generated by diversifying analyses (cross-linkers, mass spectrometry analyses, software) performed on organelles isolated from human HEK293 cells. Here, we show how the ~30,000 low-resolution distance constraints generated in near-native proteoforms can be used to uniquely (1) contextualise regions within existing experimental protein structures, (2) annotate interfaces in PPIs and multi-protein complexes, and (3) validate structures predicted by computational modellers like AlphaFold. Finally, this thesis reports the use of quantitative XL-MS to explore links between gene function and cellular phenotype, comparing wild-type yeast with a highly pleiotropic deletion strain (Δhpm1) using SILAC multiplexing and PIR cross-linking of intact cells. The untargeted comparison of structural conformations and PPIs uniquely enabled insights into phenotypes entirely invisible to investigation of protein abundance alone. This thesis will therefore argue that XL-MS is the missing link in the systems biology toolbox.

  • (2022) Gutierrez Chavez, Carolina
    Thesis
    Microbial motility is a survival strategy. Bacteria utilise motility in growth and reproduction to protect against desiccation and antibiotics, defend against competitors, colonise new habitats, and find nutrient-rich environments. Antarctica is the most extreme and pristine region on Earth. Here, soils are exposed to low temperatures, considerable levels of UV radiation, strong winds, extreme drought, and low availability of nutrients. Currently, there are no reports of motility in polar soil bacteria. Due to the extreme conditions in the Antarctic continent, we used these polar desert soils as a study model. We hypothesise that Antarctic soils are an ideal environment for bacteria to perform motility to find more favourable conditions. In this thesis, we describe for the first-time mechanisms of motility by Antarctic soil bacteria. As model microorganisms, we selected bacteria from the genera Streptomyces and Arthrobacter, belonging to the phylum Actinomycetota, the most abundant in East Antarctic soils. The first aim was to investigate the incidence and behaviour of Antarctic Streptomyces performing exploration. The genus Streptomyces had been described as a group of sessile bacteria. In 2017, the phenomenon of Streptomyces exploration was described for the first-time as a mechanism of translocation performed by Streptomyces cells through biotic and abiotic surfaces to facilitate access to distant nutrients. It was reported that the incidence of wild-type Streptomyces strains exhibiting exploration was ~10%. In addition, two critical conditions involved in the exploration process were described, glucose depletion and alkaline pH in the medium produced by the synthesis of volatile organic compounds (VOCs). Here, we screened 57 Streptomyces strains previously isolated from four sites in Eastern Antarctica. We found that 22.8% did not exhibit exploration capabilities, and 19.4% showed exploration behaviour in glucose depletion and alkaline environments. In contrast, 57.8% exhibited exploration at neutral pH or in the presence of glucose. These findings about the incidence of glucose-independent exploration suggest that the exploratory behaviour might be encouraged by searching for alternative carbon sources due to the low nutrient availability in East Antarctic soils. The second aim was to provide insight into potential compounds involved in Streptomyces exploration. Here, we obtained a fraction with emulsifying, antimicrobial, and haemolytic activities from the secretome of Streptomyces INR7 explorer cells. LC-MS analysis of the fraction and bioactive predictors revealed that a LysM-containing peptide with amphipathic properties is the responsible for the antibacterial and haemolytic activities. Furthermore, genomic annotation and sequence alignment indicate that the peptide is part of a protein belonging to the resuscitation-promoting factors family, contributing to physiological processes of cell wall remodelling and metabolic activation of dormant cells. The third aim was to describe whether Antarctic Arthrobacter isolates can use microbial hitchhiking as a motility strategy to migrate across the fungal hyphae of Antarctomyces psychrotrophicus. So far, Arthrobacter bacteria have been associated with active motility, also known as flagella-dependent motility. Flagella-assisted displacement is typical in aqueous environments; however, East Antarctic soils are exposed to arid and hyperarid conditions, suggesting that the motility of Arthrobacter isolates from these polar desert soils might be challenging. Here, we found that microbial hitchhiking facilitates the migration of Arthrobacter strains previously isolated from Antarctic soils. Hitchhiking is a form of transportation where microorganisms with null or limited motility, known as 'hitchhikers' or 'riders', use the motility of nearby motile organisms known as 'carriers' or 'host' to move. In soils, fungi facilitate the migration of bacteria over short and long distances by forming 'networks' or 'highways' on which bacteria can travel actively, passively or by direct attachment to the fungal hyphae. By using SEM, motility screening, flagella identification and hitchhiking assays, we found that of 17 Arthrobacter strains examined, 14 migrated through the fungus A. psychrotrophicus. The results suggest that Arthrobacter isolates migrated by three mechanisms: two strains travelled flagella-dependent motility, seven isolates translocated by flagella-independent motility and five strains migrated by direct attachment to the fungal surface. These findings provide evidence that Antarctic soil bacteria, specifically members of the genera Streptomyces and Arthrobacter, exhibit a high incidence of motility. We propose that motility could be a survival strategy used by bacteria to cope with the extreme conditions in Antarctica.

  • (2022) Guan, Peiyuan
    Thesis
    Cathode is the key component in lithium-ion batteries (LIBs) and it determines the performance of LIBs to a large extent. Recently, layered-structure Ni-rich cathode has attracted concentrated research attention due to its high theoretical capacity and energy density, which showed great potential as an alternative for the current dominant LiCoO2 in the energy market. Intrinsically, the high Ni content led to an excellent discharge capacity; however, the high reactivity of Ni also caused an capacity fading resulting from the undesired side reactions during prolonged cycling. Therefore, a trade-off between high capacity and long cycle life obstruction of the commercializing process of Ni-rich cathode in modern LIBs. In this case, this work attempt to employing surface modification strategy to stabilize the cyclability of Ni-rich cathodes by perovskite oxides. Because they provide a variety of outstanding physical and chemical properties. Most importantly, several materials, including metal oxide, fluoride, phosphate, etc. have been investigated as surface coating layer for the electrochemical property enhancement; however, perovskite oxide is still rarely mentioned. THus, this work firstly used a typical perovskite oxide, strontium titanate (STO) and its diverse modified forms, as surface modifier coated onto Ni-rich cathodes, respectively. In detail, chapter 4 demonstrates that the STO surface coating on NCM811 could effectively enhance its cycling stability. The effect of the heat treatment after perovskite oxide surface coating is studied and disclosed in chapter 5. In chapter 6, NCA is covered by STO with the defect-rich surface, exhibiting a better rate performance due to the higher electronic and ionic conductivity possessed by the coating layer. At last, as-prepared Nb-doped STO onto NCM811 could act as a buffer layer to suppress the dissolution of transition metal ions resulting from the electrolyte decomposed HF attacking and robust the Li diffusion channel during the charge-discharge process. The current study offers a systematically understanding of the positive effect of perovskite oxide materials-based surface modification on Ni-rich cathodes. It confirms the feasibility of improving the electrochemical performances of Ni-rich oxides by preventing the deleterious side reactions accompanied by reducing Li residues on the cathode surface, which is of great significance to the optimization of the cathode material for next-generation LIB for electric vehicles.

  • (2022) Nguyen, Thi Cam Phu
    Thesis
    The study of mechanical properties of materials (stiffness, toughness, and so on) using scanning probe microscopy (SPM) methods has received increased interest over the past few years. Atomic force microscopy (AFM) is an SPM method to image different properties of a wide range of materials down to the atomic scale. This thesis focuses on an in-depth description of various AFM-based methods to characterize the mechanical properties of biomaterials and ferroic materials on the nanometer scale. The high-order structures that form natural hierarchical shapes are claimed to be the main factor to enhance the extraordinary mechanical properties of biological structures. In this thesis, we are using three different types of AFM-based techniques (consisting of contact resonance force microscopy, force-distance map, and nanoindentation) and related fitting methods to analyse the mechanical properties of two different biomaterials, including (1) Paua abalone shell and (2) Tonkin bamboo. By combining those methods, we affirm the quantitativeness of our mechanical measurements. The obtained results reveal the detailed mechanical properties of the hierarchical structure of biomaterials and provide a strategy for accurately testing the nanoscale mechanical properties of advanced composite materials. To investigate the pressure-induced mechanical changes on the ferroelectric lead titanate, PbTiO3, single crystal, we used AFM methods to characterize the ferroelectric 90- and 180-degree in-plane and out-of-plane domain walls and observe that, despite their separation mechanically identical domains, the walls appear different in mechanical responses compared to the domains. Moreover, for the first time, we study the crackling noise concept at the length scale of a few nanometres of the ferroelectric PbTiO3 domain wall. It represents that the ultimate functional feature can be potentially exploited for new concepts in information storage and processing, sensing, and actuating. In general, these results indicate that SPM methods can provide comprehensive information and a deep insight into unique properties in a wide range of materials and their applicability in nanoscale regimes, and guide new developments on promising nanoscale devices.

  • (2022) Sah, Saroj
    Thesis
    Interactions between neurons are mediated by cell adhesion molecules (CAMs). NCAM2 and NEGR1 are two CAMs, which accumulate in synapses. Abnormal expression of these synaptic CAMs is associated with behavioral abnormalities and neurodevelopmental disorders in humans. The effects caused by deficiency in these CAMs in the brain remain, however, unclear. To better understand human conditions associated with the loss of NCAM2 and NEGR1, in this thesis, we analyzed the behavior of NCAM2 and NEGR1 deficient mice and performed immunohistochemical analyses of the brain to study the underlying mechanisms of these effects. We found that NCAM2 deficiency in mice leads to the impairment in short-term memory, mild cognitive deficit, and causes an increase in olfactory acuity and repetitive and self-grooming behaviors. Our immunohistochemical studies showed shortening of the infrapyramidal bundle of the mossy fibers in the hippocampus of the NCAM2 knockout mice suggesting axonal guidance defects. Similar axon guidance defects and changes in behavior were also observed in mice deficient in BACE1, an enzyme involved in processing of NCAM2. Further analysis showed changes in distribution and a reduction in levels of BACE1 protein in the hippocampus in NCAM2 knockout mice. Additionally, cell culture studies showed that NCAM2 knockout neurons were characterized by altered organization of the Golgi body organelles and lower levels of the microtubule-associated proteins tau and CRMP2, which are required for transporting protein cargoes and maintaining the cytoskeleton. We observed spatial and short-term memory impairment, hyposmia, and a reduction in motivation towards highly palatable food rewards in NEGR1 knockout mice. These mice had lower densities of synapses in the hippocampus, particularly of those formed by mossy fibers. The overall size of the suprapyramidal bundle of mossy fibers was reduced in NEGR1 knockout mice. These effects were accompanied by the deposition of alpha-synuclein aggregates in the hippocampus. Similarly, the density of inhibitory synapses was reduced in the CA3 pyramidal cell layer of the hippocampus and arcuate nucleus of hypothalamus, which is involved in regulating the feeding behavior. In conclusion, we found that NCAM2 and NEGR1 deficiency causes synaptic changes in the brain, which are accompanied by abnormalities in learning, suggesting that both proteins are involved in regulating neuronal development and plasticity. Our data indicate that NCAM2 and NEGR1 deficiency can directly contribute to neurodevelopmental and other types of disorders in people with variations in the genes coding for NCAM2 and NEGR1.

  • (2022) Guo, Haocheng
    Thesis
    To develop faradaic electrodes that integrate advantages of both battery (high capacity), and supercapacitor (fast rate and excellent cycle life) is revolutionary to transform our use of electrical energy, but presents a grand challenge in energy storage. Because their origins are intrinsically conflicting: high capacity requires in-depth redox reactions and longer diffusion distance of ion-charge-carriers, but the corresponding kinetics typically slow down as consequences. Recently, the emerging proton electrochemistry facilitates developments of batteries where proton/hydronium serve as ion-charge-carrier (named as proton batteries) and offers new opportunities for the long pursuit. This thesis aims to understand fundamental working principles of proton electrochemistry, design novel electrode-materials and electrolytes, and correspondingly develop full batteries. Charge storage controlled by diffusion and phase transformation of electrodes are representative indicators of sluggish kinetics in battery chemistries. However, fast rate-capabilities are reached in a α-MoO3 electrode that presents both features associating with protons. In Chapter 2 and 3, this unique topochemistry is disclosed to involve sophisticated ion-electrode-interactions and contains two key steps: hydronium adsorption on surface, and the subsequent naked proton insertion in bulk electrode lattices to trigger irreversible structure transformation to hydrogen molybdenum bronzes (HMBs) from the parent MoO3. Following rearrangements take place only among HMBs phases and present high reversibility and kinetics, therefore structural explanations to the fast rate-capability are provided. At electrode-electrolyte-interfaces, hydronium is determined as the active ion-charge-carrier to initiate charge transfer as well as surface hydration, where water adsorption/expelling with reduced polarizations and enhanced kinetics is accompanied in the meantime. Otherwise, water activities influence the basic electrochemical properties and induce material-dissolutions during functioning. Material pseudocapacitance is an alternative strategy to achieve faradaic electrodes of both high capacity and rate, where the intercalation pseudocapacitance is considered the most promising because of the full involvement of bulk reactions. In Chapter 4, the advantages of integrated intercalation pseudocapacitance and proton electrochemistry are disclosed, via the studies of proton redox chemistry in hexagonal MoO3 (h-MoO3). As a structure isomer to α-MoO3, similar properties can be found in h-MoO3 such as similar maximum proton exchange amount and an initial process out of structure rearrangements, etc. Interestingly, though surface ion de-solvation phenomena are also observed, it is identified increased crystal water in h-MoO3 after electrochemistry, which is attributed to certain hydronium intercalation into the intracrystalline tunnels. After the initial process, solid-solution proton intercalation is demonstrated in h-MoO3, accompanied with fast rate capabilities almost independent on particle sizes. Surprisingly, fast rate capabilities from proton intercalation pseudocapacitance has been demonstrated in electrodes of monocrystals over 100 μm scale. The high-potential MnO2/Mn2+ redox couple (MnO2 + 4H+ + 2e ↔ Mn2+ + 2H2O, Eθ=1.23 V, v.s. SHE) has recently attracted attentions in developing aqueous batteries, typically via electrodepositing solids on substrates for energy storage. This electrolysis reaction provides a facile and competitive cathode choice for the emerging proton batteries, because most of known electrodes either function at low potentials (due to proton reduction thermodynamics) or overlap in potentials with each other to restrict the cell voltage. However, its redox behavior is little understood in concentrated acids, and current full-cells often suffer limited cycle life (e.g., tens-of-hours). In Chapter 5, we show a homogeneous and stable MnO2 colloid electrolytes prepared by electrolysis in H2SO4 (≥ 1.0 M), and their application to achieve long life proton batteries. The colloid electrolytes enable prolonged cycling of a MnO2//MoO3 cell from 11.7 h to 33 days, and a MnO2//pyrene-4,5,9,10-tetraone cell for 489 days, which is the longest duration ever reported for proton batteries, to the best of the authors’ knowledge. Through water dilution colloids precipitate into hierarchical nanosheet spheres; Further characterizations together with deposited substrates reveal major electrolytic products as ε-MnO2 regardless of electrolytes. Colloids reform from precipitates differently with Mn2+ present/absent acids, suggesting colloid balances include both physical and chemical interactions. The results achieved in this thesis offer new fundamental insights in proton electrochemistry, introduce findings of novel electrodes and electrolytes, and demonstrate proof-of-concept application of proton batteries. The findings will guide the further search for electrode materials, exploitation of electrode performances, electrolytes, and advanced full-cell designs. It is my hope these would contribute to future energy storage techniques of high rate and capacity and beyond.