SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

An infinite-horizon robust filter for uncertain hidden Markov Models with conditional relative entropy constraints

We consider a robust filtering problem for uncertain discrete-time, homogeneous, first-order, finite-state hidden Markov models (HMMs). The class of uncertain HMMs considered is described by a conditional relative entropy constraint on measures perturbed from a nominal regular conditional probability distribution given the previous posterior state distribution and the latest measurement. Under this class of perturbations, a robust infinite horizon filtering problem is first formulated as a constrained optimization problem before being transformed via variational results into an unconstrained optimization problem; the latter can be elegantly solved using a risk-sensitive information-state based filtering.

Objectifying early-number : a visual nomenclature to express mathematical domain knowledge

To address issues of divisive ideologies in the Mathematics Education community and to subsequently advance educational practice, an alternative theoretical framework and operational model is proposed which represents a consilience of constructivist learning theories whilst acknowledging the objective but improvable nature of domain knowledge. Based upon Popper’s three-world model of knowledge, the proposed theory supports the differentiation and explicit modelling of both shared domain knowledge and idiosyncratic personal understanding using a visual nomenclature. The visual nomenclature embodies Piaget’s notion of reflective abstraction and so may support an individual’s experience-based transformation of personal understanding with regards to shared domain knowledge. Using the operational model and visual nomenclature, seminal literature regarding early-number counting and addition was analysed and described. Exemplars of the resultant visual artefacts demonstrate the proposed theory’s viability as a tool with which to characterise the reflective abstraction-based organisation of a domain’s shared knowledge. Utilising such a description of knowledge, future research needs to consider the refinement of the operational model and visual nomenclature to include the analysis, description and scaffolded transformation of personal understanding. A detailed model of knowledge and understanding may then underpin the future development of educational software tools such as computer-mediated teaching and learning environments.

Boundary weaving : the social structure and processes of organizational boundaries

Boundaries are an important field of study because they mediate almost every aspect of organizational life. They are becoming increasingly more important as organizations change more frequently and yet, despite the endemic use of the boundary metaphor in common organizational parlance, they are poorly understood. Organizational boundaries are under-theorized and researchers in related fields often simply assume their existence, without defining them. The literature on organizational boundaries is fragmented with no unifying theoretical basis. As a result, when it is recognized that an organizational boundary is "dysfunctional". there is little recourse to models on which to base remediating action. This research sets out to develop just such a theoretical model and is guided by the general question: "What is the nature of organizational boundaries?" It is argued that organizational boundaries can be conceptualised through elements of both social structure and of social process. Elements of structure include objects, coupling, properties and identity. Social processes include objectification, identification, interaction and emergence. All of these elements are integrated by a core category, or basic social process, called boundary weaving. An organizational boundary is a complex system of objects and emergent properties that are woven together by people as they interact together, objectifying the world around them, identifying with these objects and creating couplings of varying strength and polarity as well as their own fragmented identity. Organizational boundaries are characterised by the multiplicity of interconnections, a particular domain of objects, varying levels of embodiment and patterns of interaction. The theory developed in this research emerged from an exploratory, qualitative research design employing grounded theory methodology. The field data was collected from the training headquarters of the New Zealand Army using semi-structured interviews and follow up observations. The unit of analysis is an organizational boundary. Only one research context was used because of the richness and multiplicity of organizational boundaries that were present. The model arose, grounded in the data collected, through a process of theoretical memoing and constant comparative analysis. Academic literature was used as a source of data to aid theory development and the saturation of some central categories. The final theory is classified as middle range, being substantive rather than formal, and is generalizable across medium to large organizations in low-context societies. The main limitation of the research arose from the breadth of the research with multiple lines of inquiry spanning several academic disciplines, with some relevant areas such as the role of identity and complexity being addressed at a necessarily high level. The organizational boundary theory developed by this research replaces the typology approaches, typical of previous theory on organizational boundaries and reconceptualises the nature of groups in organizations as well as the role of "boundary spanners". It also has implications for any theory that relies on the concept of boundaries, such as general systems theory. The main contribution of this research is the development of a holistic model of organizational boundaries including an explanation of the multiplicity of boundaries . no organization has a single definable boundary. A significant aspect of this contribution is the integration of aspects of complexity theory and identity theory to explain the emergence of higher-order properties of organizational boundaries and of organizational identity. The core category of "boundary weaving". is a powerful new metaphor that significantly reconceptualises the way organizational boundaries may be understood in organizations. It invokes secondary metaphors such as the weaving of an organization's "boundary fabric". and provides managers with other metaphorical perspectives, such as the management of boundary friction, boundary tension, boundary permeability and boundary stability. Opportunities for future research reside in formalising and testing the theory as well as developing analytical tools that would enable managers in organizations to apply the theory in practice.

Open source innovation in physical products : advantages and disadvantages, a corporate perspective

A better understanding of Open Source Innovation in Physical Product (OSIP) might allow project managers to mitigate risks associated with this innovation model and process, while developing the right strategies to maximise OSIP outputs. In the software industry, firms have been highly successful using Open Source Innovation (OSI) strategies. However, OSI in the physical world has not been studied leading to the research question: What advantages and disadvantages do organisations incur from using OSI in physical products? An exploratory research methodology supported by thirteen semi-structured interviews helped us build a seven-theme framework to categorise advantages and disadvantages elements linked with the use of OSIP. In addition, factors impacting advantage and disadvantage elements for firms using OSIP were identified as: „h Degree of openness in OSIP projects; „h Time of release of OSIP in the public domain; „h Use of Open Source Innovation in Software (OSIS) in conjunction with OSIP; „h Project management elements (Project oversight, scope and modularity); „h Firms. Corporate Social Responsibility (CSR) values; „h Value of the OSIP project to the community. This thesis makes a contribution to the body of innovation theory by identifying advantages and disadvantages elements of OSIP. Then, from a contingency perspective it identifies factors which enhance or decrease advantages, or mitigate/ or increase disadvantages of OSIP. In the end, the research clarifies the understanding of OSI by clearly setting OSIP apart from OSIS. The main practical contribution of this paper is to provide manager with a framework to better understand OSIP as well as providing a model, which identifies contingency factors increasing advantage and decreasing disadvantage. Overall, the research allows managers to make informed decisions about when they can use OSIP and how they can develop strategies to make OSIP a viable proposition. In addition, this paper demonstrates that advantages identified in OSIS cannot all be transferred to OSIP, thus OSIP decisions should not be based upon OSIS knowledge.

Identifying and delineating information experience as a research domain : A discussion paper

A line of information and information literacy research has emerged that has a strong focus on information experience. Strengthened understanding, profiling and theorising of information experience as a specific domain of interest to information researchers is required. A focus on information experience is likely to have a major influence on the field, drawing attention to interpretive and experiential forms of research.

Effect of topic domain and task type on Web image searching

Many user studies in Web information searching have found the significant effect of task types on search strategies. However, little attention was given to Web image searching strategies, especially the query reformulation activity despite that this is a crucial part in Web image searching. In this study, we investigated the effects of topic domains and task types on user’s image searching behavior and query reformulation strategies. Some significant differences in user’s tasks specificity and initial concepts were identified among the task domains. Task types are also found to influence participant’s result reviewing behavior and query reformulation strategies.

A semi-local method for iterative depth-map refinement

We present an iterative hierarchical algorithm for multi-view stereo. The algorithm attempts to utilise as much contextual information as is available to compute highly accurate and robust depth maps. There are three novel aspects to the approach: 1) firstly we incrementally improve the depth fidelity as the algorithm progresses through the image pyramid; 2) secondly we show how to incorporate visual hull information (when available) to constrain depth searches; and 3) we show how to simultaneously enforce the consistency of the depth-map by continual comparison with neighbouring depth-maps. We show that this approach produces highly accurate depth-maps and, since it is essentially a local method, is both extremely fast and simple to implement.

Molecular structure of the phosphate mineral brazilianite NaAl3(PO4)2(OH)4 : a semi precious jewel

The phosphate mineral brazilianite NaAl3(PO4)2(OH)4 is a semi precious jewel. There are almost no minerals apart from brazilianite which are used in jewellery. Vibrational spectroscopy was used to characterize the mol. structure of brazilianite. Brazilianite is composed of chains of edge-sharing Al-O octahedra linked by P-O tetrahedra, with Na located in cavities of the framework. An intense sharp Raman band at 1019 cm-1 is attributed to the PO43- sym. stretching mode. Raman bands at 973 and 988 cm-1 are assigned to the stretching vibrations of the HOPO33- units. The IR spectra compliment the Raman spectra but show greater complexity. Multiple Raman bands are obsd. in the PO43- and HOPO33- bending region. This observation implies that both phosphate and hydrogen phosphate units are involved in the structure. Raman OH stretching vibrations are found at 3249, 3417 and 3472 cm-1. These peaks show that the OH units are not equiv. in the brazilianite structure. Vibrational spectroscopy is useful for increasing the knowledge of the mol. structure of brazilianite.

The Australian domain name registration system : a more efficient system for the promotion of liberalisation, consumer protection and growth

This thesis is about the Australian domain name system and, in particular, the principles governing the registration of domain names in the '.au' country code domain space. It examines the different types of registration systems adopted in country code domain spaces and categorises them according to the extent to which they impose restrictions on registration, ranging from restrictive to unrestrictive. A comparative analysis is made of the restrictive registration system in Australia and the United Kingdom‘s unrestrictive system.

Defining the role of phytoene synthase in carotenoid accumulation of high provitamin A bananas

Vitamin A deficiency (VAD) is a serious problem in developing countries, affecting approximately 127 million children of preschool age and 7.2 million pregnant women each year. However, this deficiency is readily treated and prevented through adequate nutrition. This can potentially be achieved through genetically engineered biofortification of staple food crops to enhance provitamin A (pVA) carotenoid content. Bananas are the fourth most important food crop with an annual production of 100 million tonnes and are widely consumed in areas affected by VAD. However, the fruit pVA content of most widely consumed banana cultivars is low (~ 0.2 to 0.5 ìg/g dry weight). This includes cultivars such as the East African highland banana (EAHB), the staple crop in countries such as Uganda, where annual banana consumption is approximately 250 kg per person. This fact, in addition to the agronomic properties of staple banana cultivars such as vegetative reproduction and continuous cropping, make bananas an ideal target for pVA enhancement through genetic engineering. Interestingly, there are banana varieties known with high fruit pVA content (up to 27.8 ìg/g dry weight), although they are not widely consumed due to factors such as cultural preference and availability. The genes involved in carotenoid accumulation during banana fruit ripening have not been well studied and an understanding of the molecular basis for the differential capacity of bananas to accumulate carotenoids may impact on the effective production of genetically engineered high pVA bananas. The production of phytoene by the enzyme phytoene synthase (PSY) has been shown to be an important rate limiting determinant of pVA accumulation in crop systems such as maize and rice. Manipulation of this gene in rice has been used successfully to produce Golden Rice, which exhibits higher seed endosperm pVA levels than wild type plants. Therefore, it was hypothesised that differences between high and low pVA accumulating bananas could be due either to differences in PSY enzyme activity or factors regulating the expression of the psy gene. Therefore, the aim of this thesis was to investigate the role of PSY in accumulation of pVA in banana fruit of representative high (Asupina) and low (Cavendish) pVA banana cultivars by comparing the nucleic acid and encoded amino acid sequences of the banana psy genes, in vivo enzyme activity of PSY in rice callus and expression of PSY through analysis of promoter activity and mRNA levels. Initially, partial sequences of the psy coding region from five banana cultivars were obtained using reverse transcriptase (RT)-PCR with degenerate primers designed to conserved amino acids in the coding region of available psy sequences from other plants. Based on phylogenetic analysis and comparison to maize psy sequences, it was found that in banana, psy occurs as a gene family of at least three members (psy1, psy2a and psy2b). Subsequent analysis of the complete coding regions of these genes from Asupina and Cavendish suggested that they were all capable of producing functional proteins due to high conservation in the catalytic domain. However, inability to obtain the complete mRNA sequences of Cavendish psy2a, and isolation of two non-functional Cavendish psy2a coding region variants, suggested that psy2a expression may be impaired in Cavendish. Sequence analysis indicated that these Cavendish psy2a coding region variants may have resulted from alternate splicing. Evidence of alternate splicing was also observed in one Asupina psy1 coding region variant, which was predicted to produce a functional PSY1 isoform. The complete mRNA sequence of the psy2b coding regions could not be isolated from either cultivar. Interestingly, psy1 was cloned predominantly from leaf while psy2 was obtained preferentially from fruit, suggesting some level of tissue-specific expression. The Asupina and Cavendish psy1 and psy2a coding regions were subsequently expressed in rice callus and the activity of the enzymes compared in vivo through visual observation and quantitative measurement of carotenoid accumulation. The maize B73 psy1 coding region was included as a positive control. After several weeks on selection, regenerating calli showed a range of colours from white to dark orange representing various levels of carotenoid accumulation. These results confirmed that the banana psy coding regions were all capable of producing functional enzymes. No statistically significant differences in levels of activity were observed between banana PSYs, suggesting that differences in PSY activity were not responsible for differences in the fruit pVA content of Asupina and Cavendish. The psy1 and psy2a promoter sequences were isolated from Asupina and Cavendish gDNA using a PCR-based genome walking strategy. Interestingly, three Cavendish psy2a promoter clones of different sizes, representing possible allelic variants, were identified while only single promoter sequences were obtained for the other Asupina and Cavendish psy genes. Bioinformatic analysis of these sequences identified motifs that were previously characterised in the Arabidopsis psy promoter. Notably, an ATCTA motif associated with basal expression in Arabidopsis was identified in all promoters with the exception of two of the Cavendish psy2a promoter clones (Cpsy2apr2 and Cpsy2apr3). G1 and G2 motifs, linked to light-regulated responses in Arabidopsis, appeared to be differentially distributed between psy1 and psy2a promoters. In the untranscribed regulatory regions, the G1 motifs were found only in psy1 promoters, while the G2 motifs were found only in psy2a. Interestingly, both ATCTA and G2 motifs were identified in the 5’ UTRs of Asupina and Cavendish psy1. Consistent with other monocot promoters, introns were present in the Asupina and Cavendish psy1 5’ UTRs, while none were observed in the psy2a 5’ UTRs. Promoters were cloned into expression constructs, driving the â-glucuronidase (GUS) reporter gene. Transient expression of the Asupina and Cavendish psy1 and psy2a promoters in both Cavendish embryogenic cells and Cavendish fruit demonstrated that all promoters were active, except Cpsy2apr2 and Cpsy2apr3. The functional Cavendish psy2a promoter (Cpsy2apr1) appeared to have activity similar to the Asupina psy2a promoter. The activities of the Asupina and Cavendish psy1 promoters were similar to each other, and comparable to those of the functional psy2a promoters. Semi-quantitative PCR analysis of Asupina and Cavendish psy1 and psy2a transcripts showed that psy2a levels were high in green fruit and decreased during ripening, reinforcing the hypothesis that fruit pVA levels were largely dependent on levels of psy2a expression. Additionally, semi-quantitative PCR using intron-spanning primers indicated that high levels of unprocessed psy2a and psy2b mRNA were present in the ripe fruit of Cavendish but not in Asupina. This raised the possibility that differences in intron processing may influence pVA accumulation in Asupina and Cavendish. In this study the role of PSY in banana pVA accumulation was analysed at a number of different levels. Both mRNA accumulation and promoter activity of psy genes studied were very similar between Asupina and Cavendish. However, in several experiments there was evidence of cryptic or alternate splicing that differed in Cavendish compared to Asupina, although these differences were not conclusively linked to the differences in fruit pVA accumulation between Asupina and Cavendish. Therefore, other carotenoid biosynthetic genes or regulatory mechanisms may be involved in determining pVA levels in these cultivars. This study has contributed to an increased understanding of the role of PSY in the production of pVA carotenoids in banana fruit, corroborating the importance of this enzyme in regulating carotenoid production. Ultimately, this work may serve to inform future research into pVA accumulation in important crop varieties such as the EAHB and the discovery of avenues to improve such crops through genetic modification.

Three carrier ambiguity resolution : distance-independent performance demonstrated using semi-generated triple frequency GPS signals

In spite of significant research in the development of efficient algorithms for three carrier ambiguity resolution, full performance potential of the additional frequency signals cannot be demonstrated effectively without actual triple frequency data. In addition, all the proposed algorithms showed their difficulties in reliable resolution of the medium-lane and narrow-lane ambiguities in different long-range scenarios. In this contribution, we will investigate the effects of various distance-dependent biases, identifying the tropospheric delay to be the key limitation for long-range three carrier ambiguity resolution. In order to achieve reliable ambiguity resolution in regional networks with the inter-station distances of hundreds of kilometers, a new geometry-free and ionosphere-free model is proposed to fix the integer ambiguities of the medium-lane or narrow-lane observables over just several minutes without distance constraint. Finally, the semi-simulation method is introduced to generate the third frequency signals from dual-frequency GPS data and experimentally demonstrate the research findings of this paper.

Feature-domain super-resolution framework for gabor-based face and iris recognition

The low resolution of images has been one of the major limitations in recognising humans from a distance using their biometric traits, such as face and iris. Superresolution has been employed to improve the resolution and the recognition performance simultaneously, however the majority of techniques employed operate in the pixel domain, such that the biometric feature vectors are extracted from a super-resolved input image. Feature-domain superresolution has been proposed for face and iris, and is shown to further improve recognition performance by capitalising on direct super-resolving the features which are used for recognition. However, current feature-domain superresolution approaches are limited to simple linear features such as Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), which are not the most discriminant features for biometrics. Gabor-based features have been shown to be one of the most discriminant features for biometrics including face and iris. This paper proposes a framework to conduct super-resolution in the non-linear Gabor feature domain to further improve the recognition performance of biometric systems. Experiments have confirmed the validity of the proposed approach, demonstrating superior performance to existing linear approaches for both face and iris biometrics.

Prediction of the wash-off of traffic related semi- and non-volatile organic compounds from urban roads under climate change influenced rainfall characteristics

Traffic generated semi and non volatile organic compounds (SVOCs and NVOCs) pose a serious threat to human and ecosystem health when washed off into receiving water bodies by stormwater. Climate change influenced rainfall characteristics makes the estimation of these pollutants in stormwater quite complex. The research study discussed in the paper developed a prediction framework for such pollutants under the dynamic influence of climate change on rainfall characteristics. It was established through principal component analysis (PCA) that the intensity and durations of low to moderate rain events induced by climate change mainly affect the wash-off of SVOCs and NVOCs from urban roads. The study outcomes were able to overcome the limitations of stringent laboratory preparation of calibration matrices by extracting uncorrelated underlying factors in the data matrices through systematic application of PCA and factor analysis (FA). Based on the initial findings from PCA and FA, the framework incorporated orthogonal rotatable central composite experimental design to set up calibration matrices and partial least square regression to identify significant variables in predicting the target SVOCs and NVOCs in four particulate fractions ranging from >300-1 μm and one dissolved fraction of <1 μm. For the particulate fractions range >300-1 μm, similar distributions of predicted and observed concentrations of the target compounds from minimum to 75th percentile were achieved. The inter-event coefficient of variations for particulate fractions of >300-1 μm were 5% to 25%. The limited solubility of the target compounds in stormwater restricted the predictive capacity of the proposed method for the dissolved fraction of <1 μm.

Diurnal Variation of Retinal Thickness with Spectral Domain OCT

Purpose. To investigate whether diurnal variation occurs in retinal thickness measures derived from spectral domain optical coherence tomography (SD-OCT). Methods. Twelve healthy adult subjects had retinal thickness measured with SD-OCT every 2 h over a 10 h period. At each measurement session, three average B-scan images were derived from a series of multiple B-scans (each from a 5 mm horizontal raster scan along the fovea, containing 1500 A-scans/B-scan) and analyzed to determine the thickness of the total retina, as well as the thickness of the outer retinal layers. Average thickness values were calculated at the foveal center, at the 0.5 mm diameter foveal region, and for the temporal parafovea (1.5 mm from foveal center) and nasal parafovea (1.5 mm from foveal center). Results. Total retinal thickness did not exhibit significant diurnal variation in any of the considered retinal regions (p > 0.05). Evidence of significant diurnal variation was found in the thickness of the outer retinal layers (p < 0.05), with the most prominent changes observed in the photoreceptor layers at the foveal center. The photoreceptor inner and outer segment layer thickness exhibited mean amplitude (peak to trough) of daily change of 7 ± 3 μm at the foveal center. The peak in thickness was typically observed at the third measurement session (mean measurement time, 13:06). Conclusions. The total retinal thickness measured with SD-OCT does not exhibit evidence of significant variation over the course of the day. However, small but significant diurnal variation occurs in the thickness of the foveal outer retinal layers.