Synthesis of functional nanoassemblies in reactive plasmas

Synthesis of various functional nanoassemblies, by using a combination of low-pressure reactive plasma-enhanced chemical deposition and plasma-assisted rf magnetron sputtering deposition is reported. This paper details how selective generation and manipulation of the required building blocks and management of unwanted nanoparticle contaminants, can be used for plasma-aided nanofabrication of carbon nanotip microemitter structures, ultra-high aspect ratio semiconductor nanowires, ordered quantum dot arrays, and microporous hydroxyapatite bioceramics. Emerging challenges of the plasma-aided synthesis of functional nanofilms and nanoassemblies are also discussed.

Integrated plasma-aided nanofabrication facility: Operation, parameters, and assembly of quantum structures and functional nanomaterials

The development, operation, and applications of two configurations of an integrated plasma-aided nanofabrication facility (IPANF) comprising low-frequency inductively coupled plasma-assisted, low-pressure, multiple-target RF magnetron sputtering plasma source, are reported. The two configurations of the plasma source have different arrangements of the RF inductive coil: a conventional external flat spiral "pancake" coil and an in-house developed internal antenna comprising two orthogonal RF current sheets. The internal antenna configuration generates a "unidirectional" RF current that deeply penetrates into the plasma bulk and results in an excellent uniformity of the plasma over large areas and volumes. The IPANF has been employed for various applications, including low-temperature plasma-enhanced chemical vapor deposition of vertically aligned single-crystalline carbon nanotips, growth of ultra-high aspect ratio semiconductor nanowires, assembly of optoelectronically important Si, SiC, and Al1-xInxN quantum dots, and plasma-based synthesis of bioactive hydroxyapatite for orthopedic implants.

Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy

While genomics provide important information about the somatic genetic changes, and RNA transcript profiling can reveal important expression changes that correlate with outcome and response to therapy, it is the proteins that do the work in the cell. At a functional level, derangements within the proteome, driven by post-translational and epigenetic modifications, such as phosphorylation, is the cause of a vast majority of human diseases. Cancer, for instance, is a manifestation of deranged cellular protein molecular networks and cell signaling pathways that are based on genetic changes at the DNA level. Importantly, the protein pathways contain the drug targets in signaling networks that govern overall cellular survival, proliferation, invasion and cell death. Consequently, the promise of proteomics resides in the ability to extend analysis beyond correlation to causality. A critical gap in the information knowledge base of molecular profiling is an understanding of the ongoing activity of protein signaling in human tissue: what is activated and “in use” within the human body at any given point in time. To address this gap, we have invented a new technology, called reverse phase protein microarrays, that can generate a functional read-out of cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This “wiring diagram” can serve as the basis for both, selection of a therapy and patient stratification.

Ion-assisted functional monolayer coating of nanorod arrays in hydrogen plasmas

Uniformity of postprocessing of large-area, dense nanostructure arrays is currently one of the greatest challenges in nanoscience and nanofabrication. One of the major issues is to achieve a high level of control in specie fluxes to specific surface areas of the nanostructures. As suggested by the numerical experiments in this work, this goal can be achieved by manipulating microscopic ion fluxes by varying the plasma sheath and nanorod array parameters. The dynamics of ion-assisted deposition of functional monolayer coatings onto two-dimensional carbon nanorod arrays in a hydrogen plasma is simulated by using a multiscale hybrid numerical simulation. The numerical results show evidence of a strong correlation between the aspect ratios and nanopattern positioning of the nanorods, plasma sheath width, and densities and distributions of microscopic ion fluxes. When the spacing between the nanorods and/or their aspect ratios are larger, and/or the plasma sheath is wider, the density of microscopic ion current flowing to each of the individual nanorods increases, thus reducing the time required to apply a functional monolayer coating down to 11 s for a 7-μm-wide sheath, and to 5 s for a 50-μm-wide sheath. The computed monolayer coating development time is consistent with previous experimental reports on plasma-assisted functionalization of related carbon nanostructures [B. N. Khare et al., Appl. Phys. Lett. 81, 5237 (2002)]. The results are generic in that they can be applied to a broader range of plasma-based processes and nanostructures, and contribute to the development of deterministic strategies of postprocessing and functionalization of various nanoarrays for nanoelectronic, biomedical, and other emerging applications.

Brain decoding based on functional magnetic resonance imaging using machine learning : a comparative study

Brain decoding of functional Magnetic Resonance Imaging data is a pattern analysis task that links brain activity patterns to the experimental conditions. Classifiers predict the neural states from the spatial and temporal pattern of brain activity extracted from multiple voxels in the functional images in a certain period of time. The prediction results offer insight into the nature of neural representations and cognitive mechanisms and the classification accuracy determines our confidence in understanding the relationship between brain activity and stimuli. In this paper, we compared the efficacy of three machine learning algorithms: neural network, support vector machines, and conditional random field to decode the visual stimuli or neural cognitive states from functional Magnetic Resonance data. Leave-one-out cross validation was performed to quantify the generalization accuracy of each algorithm on unseen data. The results indicated support vector machine and conditional random field have comparable performance and the potential of the latter is worthy of further investigation.

Anterior temporal cortex and semantic memory : reconciling findings from neuropsychology and functional imaging

Studies of semantic impairment arising from brain disease suggest that the anterior temporal lobes are critical for semantic abilities in humans; yet activation of these regions is rarely reported in functional imaging studies of healthy controls performing semantic tasks. Here, we combined neuropsychological and PET functional imaging data to show that when healthy subjects identify concepts at a specific level, the regions activated correspond to the site of maximal atrophy in patients with relatively pure semantic impairment. The stimuli were color photographs of common animals or vehicles, and the task was category verification at specific (e.g., robin), intermediate (e.g., bird), or general (e.g., animal) levels. Specific, relative to general, categorization activated the antero-lateral temporal cortices bilaterally, despite matching of these experimental conditions for difficulty. Critically, in patients with atrophy in precisely these areas, the most pronounced deficit was in the retrieval of specific semantic information.

Comparison of block and event-related experimental designs in diffusion-weighted functional MRI

PURPOSE To compare diffusion-weighted functional magnetic resonance imaging (DfMRI), a novel alternative to the blood oxygenation level-dependent (BOLD) contrast, in a functional MRI experiment. MATERIALS AND METHODS Nine participants viewed contrast reversing (7.5 Hz) black-and-white checkerboard stimuli using block and event-related paradigms. DfMRI (b = 1800 mm/s2 ) and BOLD sequences were acquired. Four parameters describing the observed signal were assessed: percent signal change, spatial extent of the activation, the Euclidean distance between peak voxel locations, and the time-to-peak of the best fitting impulse response for different paradigms and sequences. RESULTS The BOLD conditions showed a higher percent signal change relative to DfMRI; however, event-related DfMRI showed the strongest group activation (t = 21.23, P < 0.0005). Activation was more diffuse and spatially closer to the BOLD response for DfMRI when the block design was used. DfMRIevent showed the shortest TTP (4.4 +/- 0.88 sec). CONCLUSION The hemodynamic contribution to DfMRI may increase with the use of block designs.

Examining the role of within functional area resource–capability complementarity in achieving customer and product-based performance outcomes

Adopting both the resource-based view and dynamic capability theory this study advances the contention that firms must possess both resources and capabilities at a superior level to achieve superior customer and product performance. To examine this contention this study investigates the individual effect of the complementarity between marketing resources and capability and complementarity between innovation resources and capability on customer and product performance respectively. The results of a survey of 171 B2B manufacturing firms show a significant main effect for complementarity between marketing resources–capability and complementarity between innovation resources–capability on customer and product performance. The findings also show that complementarity marketing resources–capability has a stronger positive relationship with customer performance than with product performance, while complementarity between innovation resources–capability has a stronger positive relationship with product performance than with customer performance.

JK1 (FAM134B) represses cell migration in colon cancer : a functional study of a novel gene

Background JK1 is a novel cancer-related gene with unknown functional role in carcinogenesis. The aim of this study is to investigate the role of JK1 gene in carcinogenesis in an in vitro cell proliferation and migration analysis model. Methods Small hairpin RNAs (shRNA) were designed to knock-down JK1 expression in colon cancer cell line (SW480) using transduction ready lentiviral particles. Cell proliferation and cell migration assays were performed on multiple extracellular matrices to investigate the cellular effects of JK1 in colon cancer cells. A non-cancer colonic epithelial cell line (FHC) was used to compare the expression of JK1 in cancer cell line. Results JK1 knock-down did not affect cellular proliferation or survival in colon cancer. However, the manipulation increased cancer cell migration rates on collagen and fibronectin substrates. Conclusions JK1 was shown for the first time to have a functional role in the pathogenesis of colon cancer. The results imply that JK1 represses the capacity of cancer cells to migrate within their tissue. They also concurred with the previous findings of JK1 activity correlations with clinical and pathological features in colon cancer. The capacity may have utility as a means to prevent cancer cells forming metastases.

Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation

Ataxia oculomotor apraxia type 2 (AOA2) is an autosomal recessive neurodegenerative disorder characterized by cerebellar ataxia and oculomotor apraxia. The gene mutated in AOA2, SETX, encodes senataxin, a putative DNA/RNA helicase which shares high homology to the yeast Sen1p protein and has been shown to play a role in the response to oxidative stress. To investigate further the function of senataxin, we identified novel senataxin-interacting proteins, the majority of which are involved in transcription and RNA processing, including RNA polymerase II. Binding of RNA polymerase II to candidate genes was significantly reduced in senataxin deficient cells and this was accompanied by decreased transcription of these genes, suggesting a role for senataxin in the regulation/modulation of transcription. RNA polymerase II-dependent transcription termination was defective in cells depleted of senataxin in keeping with the observed interaction of senataxin with poly(A) binding proteins 1 and 2. Splicing efficiency of specific mRNAs and alternate splice-site selection of both endogenous genes and artificial minigenes were altered in senataxin depleted cells. These data suggest that senataxin, similar to its yeast homolog Sen1p, plays a role in coordinating transcriptional events, in addition to its role in DNA repair.

Development of gas sensing technology for ground and airborne applications powered by solar energy : methodology and experimental results

Monitoring gases for environmental, industrial and agricultural fields is a demanding task that requires long periods of observation, large quantity of sensors, data management, high temporal and spatial resolution, long term stability, recalibration procedures, computational resources, and energy availability. Wireless Sensor Networks (WSNs) and Unmanned Aerial Vehicles (UAVs) are currently representing the best alternative to monitor large, remote, and difficult access areas, as these technologies have the possibility of carrying specialised gas sensing systems, and offer the possibility of geo-located and time stamp samples. However, these technologies are not fully functional for scientific and commercial applications as their development and availability is limited by a number of factors: the cost of sensors required to cover large areas, their stability over long periods, their power consumption, and the weight of the system to be used on small UAVs. Energy availability is a serious challenge when WSN are deployed in remote areas with difficult access to the grid, while small UAVs are limited by the energy in their reservoir tank or batteries. Another important challenge is the management of data produced by the sensor nodes, requiring large amount of resources to be stored, analysed and displayed after long periods of operation. In response to these challenges, this research proposes the following solutions aiming to improve the availability and development of these technologies for gas sensing monitoring: first, the integration of WSNs and UAVs for environmental gas sensing in order to monitor large volumes at ground and aerial levels with a minimum of sensor nodes for an effective 3D monitoring; second, the use of solar energy as a main power source to allow continuous monitoring; and lastly, the creation of a data management platform to store, analyse and share the information with operators and external users. The principal outcomes of this research are the creation of a gas sensing system suitable for monitoring any kind of gas, which has been installed and tested on CH4 and CO2 in a sensor network (WSN) and on a UAV. The use of the same gas sensing system in a WSN and a UAV reduces significantly the complexity and cost of the application as it allows: a) the standardisation of the signal acquisition and data processing, thereby reducing the required computational resources; b) the standardisation of calibration and operational procedures, reducing systematic errors and complexity; c) the reduction of the weight and energy consumption, leading to an improved power management and weight balance in the case of UAVs; d) the simplification of the sensor node architecture, which is easily replicated in all the nodes. I evaluated two different sensor modules by laboratory, bench, and field tests: a non-dispersive infrared module (NDIR) and a metal-oxide resistive nano-sensor module (MOX nano-sensor). The tests revealed advantages and disadvantages of the two modules when used for static nodes at the ground level and mobile nodes on-board a UAV. Commercial NDIR modules for CO2 have been successfully tested and evaluated in the WSN and on board of the UAV. Their advantage is the precision and stability, but their application is limited to a few gases. The advantages of the MOX nano-sensors are the small size, low weight, low power consumption and their sensitivity to a broad range of gases. However, selectivity is still a concern that needs to be addressed with further studies. An electronic board to interface sensors in a large range of resistivity was successfully designed, created and adapted to operate on ground nodes and on-board UAV. The WSN and UAV created were powered with solar energy in order to facilitate outdoor deployment, data collection and continuous monitoring over large and remote volumes. The gas sensing, solar power, transmission and data management systems of the WSN and UAV were fully evaluated by laboratory, bench and field testing. The methodology created to design, developed, integrate and test these systems was extensively described and experimentally validated. The sampling and transmission capabilities of the WSN and UAV were successfully tested in an emulated mission involving the detection and measurement of CO2 concentrations in a field coming from a contaminant source; the data collected during the mission was transmitted in real time to a central node for data analysis and 3D mapping of the target gas. The major outcome of this research is the accomplishment of the first flight mission, never reported before in the literature, of a solar powered UAV equipped with a CO2 sensing system in conjunction with a network of ground sensor nodes for an effective 3D monitoring of the target gas. A data management platform was created using an external internet server, which manages, stores, and shares the data collected in two web pages, showing statistics and static graph images for internal and external users as requested. The system was bench tested with real data produced by the sensor nodes and the architecture of the platform was widely described and illustrated in order to provide guidance and support on how to replicate the system. In conclusion, the overall results of the project provide guidance on how to create a gas sensing system integrating WSNs and UAVs, how to power the system with solar energy and manage the data produced by the sensor nodes. This system can be used in a wide range of outdoor applications, especially in agriculture, bushfires, mining studies, zoology, and botanical studies opening the way to an ubiquitous low cost environmental monitoring, which may help to decrease our carbon footprint and to improve the health of the planet.

Recovering Functional Integrity in Pastures Dominated by an Invasive Grass Species

Exotic grasses have been introduced in countries worldwide for pasture improvement, soil stabilisation and ornamental purposes. Some of these introductions have proven successful, but many have not (Cook & Dias 2006). In Australia, the Commonwealth Plant Introduction Scheme was initiated in 1929, and over-time introduced more than 5000 species of grasses, legumes and other forage and browse plants (Cook & Dias 2006). Lonsdale (1994) suggested that, in tropical Australia, 13% of introductions have become a problem, with only 5% being considered useful for agriculture. Low (1997) suggested that 5 out of 18 of Australia's worst tropical environmental weeds were intentionally introduced as pasture grasses. The spread and dominance of invasive grass species that degrade the quality of pastures for production can impact significantly on the livelihoods of small proprietors. Although Livestock grazing contributes only a small percentage to the world's GDP (1.5%), maintaining the long-term stability of this industry is crucial because of the high social and environmental consequence of a collapse. One billion of the world's poor are dependent on livestock grazing for food and income with this industry occupying more than 25% of the world's land base (Steinfeld et al. 2006). The ling-term sustainability of livestock grazing is also crucial for the environment. A recent FAO report attributed livestock production as a major cause of five of the most serious environmental problems: global warming, land degredation, air and water pollution, and the loss of biodiversity (Steinfeld et al. 2006). For these reasons, finding more effective approaches that guide the sustainable management of pastures is urgently needed. In Australia more than 55% of land use is for livestock grazing by sheelp and/or cattle. This land use dominate in the semi-arid and arid regions where rainfall and soil conditions are marginal for production (Commonwealth of Australia 2004). Although the level of agriculture production by conglomerates is increasing, the majority of livestock grazing within Australia remains family owned and operated (Commonwealth of Australia 2004). The sustainability of production from a grazed pasture is dependent on its botanical composition (Kemp & Dowling 1991, Kemp et al. 1996). In a grazed pasture, the dominance of an invasive grass species can impact on the functional integrity of the ecosystem, including production and nutrient cycling; wwhich will in turn, affect the income of proprietors and the ability of the system to recover from disturbance and environmental change. In Australia, $0.3 billion is spent on weed control in livestock production, but despite this substantial investment $1.9 billion is still lost in yield as a result of weeds (Sinden et al. 2004). In this paper, we adaprt a framework proposed for the restoration of degraded rainforest communities (Lamb & Gilmour 2003, Lamb et al. 2005) to compare and contrast options for recovering function integrity (i.e. a diverse set of desirable plant species that maintain key ecological processes necessary for sustainable production and nutrient cycling) within pasture communities dominated by an invasive grass species. To do this, we uase a case-study of the invasion of Eragrostis curvula (Africal lovegrss; hereafter, Lovegrass), a serious concern in Australian agricultural communities (Parsons and Cuthbertson 1992). The spread and dominance of Lovegrass is a problem because its low palatability, low nutritional content and competitiveness affect the livelihood of graziers by reducing the diversity of other plant species. We conclude by suggesting modifications to this framework for pasture ecosystems to help increase the effiency of strategies to protect functional integrity and balance social/economic and biodiversity values.

Centrobin regulates the assembly of functional mitotic spindles

The proper function of the spindle is crucial to the high fidelity of chromosome segregation and is indispensable for tumor suppression in humans. Centrobin is a recently identified centrosomal protein that has a role in stabilizing the microtubule structure. Here we functionally characterize the defects in centrosome integrity and spindle assembly in Centrobin-depleted cells. Centrobin-depleted cells show a range of spindle abnormalities including unfocused poles that are not associated with centrosomes, S-shaped spindles and mini spindles. These cells undergo mitotic arrest and subsequently often die by apoptosis, as determined by live cell imaging. Co-depletion of Mad2 relieves the mitotic arrest, indicating that cells arrest due to a failure to silence the spindle checkpoint in metaphase. Consistent with this, Centrobin-depleted metaphase cells stained positive for BubR1 and BubR1 S676. Staining with a panel of centrosome markers showed a loss of centrosome anchoring to the mitotic spindle. Furthermore, these cells show less cold-stable microtubules and a shorter distance between kinetochore pairs. These results show a requirement of Centrobin in maintaining centrosome integrity, which in turn promotes anchoring of mitotic spindle to the centrosomes. Furthermore, this anchoring is required for the stability of microtubule–kinetochore attachments and biogenesis of tension-ridden and properly functioning mitotic spindle.

An investigation of functional diversity of endogenous cellulase and expression of other digestive enzyme genes in freshwater crayfish (Cherax) species

The project evaluated potential of soluble cellulose as a cheap feed ingredient for major farmed Australian freshwater crayfish species testing their growth performance, digestive enzyme activity and digestive enzyme gene expression patterns. Test animals showed an innate capacity to utilise a range of carbohydrate sources including complex structural polysaccharides. Results suggest that more plant-derived ingredient can be incorporated in formulated low-cost feeds for the culture industry.

The functional significance of fruit exocarp on host selection and oviposition by Queensland fruit fly, Bactrocera tryoni (Froggatt) (Tephritidae: Diptera)

Queensland fruit fly is Australia's most serious insect pest of horticulture. The fly lays its eggs into fruit, where they hatch into maggots which destroy the fruit. Understanding egg laying behaviour, known as oviposition, is a critical but under-researched aspect of fruit fly biology. This thesis focused on three aspects of oviposition: the role of fruit peel as a physical barrier to oviposition; the quality of fruit for maggot development; and the structure and wear of the egg laying organ – the ovipositor. Results showed that flies selected fruit based on their suitability for offspring survival, not because of the softness or hardness of fruit peel. Previously reported use of holes or wounds in fruit peel by ovipositing females was determined to be a mechanism which saved the female time, not a mechanism to reduce ovipositor wear. The results offer insights into the evolution of host use by fruit flies and their sustainable management.