Spatially stratified sampling using auxiliary information for geostatistical mapping

This paper presents a method of spatial sampling based on stratification by Local Moran’s I i calculated using auxiliary information. The sampling technique is compared to other design-based approaches including simple random sampling, systematic sampling on a regular grid, conditional Latin Hypercube sampling and stratified sampling based on auxiliary information, and is illustrated using two different spatial data sets. Each of the samples for the two data sets is interpolated using regression kriging to form a geostatistical map for their respective areas. The proposed technique is shown to be competitive in reproducing specific areas of interest with high accuracy.

CDKN2A is not the principal target of deletions on the short arm of chromosome 9 in neuroendocrine (Merkel cell) carcinoma of the skin

The majority of small-cell lung cancers (SCLCs) express p16 but not pRb. Given our previous study showing loss of pRb in Merkel cell carcinoma (MCC)/neuroendocrine carcinoma of the skin and the clinicopathological similarities between SCLC and MCC, we wished to determine if this was also the case in MCC. Twenty-nine MCC specimens from 23 patients were examined for deletions at 10 loci on 9p and 1 on 9q. No loss of heterozygosity (LOH) was seen in 9 patients including 2 for which tumour and cell line DNAs were examined. Four patients had LOH for all informative loci on 9p. Ten tumours showed more limited regions of loss on 9p, and from these 2 common regions of deletion were determined. Half of all informative cases had LOH at D9S168, the most telomeric marker examined, and 3 specimens showed loss of only D9S168. A second region (IFNA-D9S126) showed LOH in 10 (44%) cases, and case MCC26 showed LOH for only D9S126, implicating genes centromeric of the CDKN2A locus. No mutations in the coding regions of p16 were seen in 7 cell lines tested, and reactivity to anti-p16 antibody was seen in all 11 tumour specimens examined and in 6 of 7 cell lines from 6 patients. Furthermore, all cell lines examined reacted with anti-p14(ARF) antibody. These results suggest that neither transcript of the CDKN2A locus is the target of deletions on 9p in MCC and imply the existence of tumour-suppressor genes mapping both centromeric and telomeric of this locus.

Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development

Cytogenetic and loss of heterozygosity (LOH) studies have long indicated the presence of a tumor suppressor gene (TSG) on 9p involved in the development of melanoma. Although LOH at 9p has been reported in approximately 60% of melanoma tumors, only 5-10% of these tumors have been shown to carry CDKN2A mutations, raising the possibility that another TSG involved in melanoma maps to chromosome 9p. To investigate this possibility, a panel of 37 melanomas derived from 35 individuals was analyzed for CDKN2A mutations by single-strand conformation polymorphism analysis and sequencing. The melanoma samples were then typed for 15 markers that map to 9p13-24 to investigate LOH trends in this region. In those tumors demonstrating retention of heterozygosity at markers flanking CDKN2A and LOH on one or both sides of the gene, multiplex microsatellite PCR was performed to rule out homozygous deletion of the region encompassing CDKN2A. CDKN2A mutations were found in tumors from 5 patients [5 (14%) of 35], 4 of which demonstrated LOH across the entire region examined. The remaining tumor with no observed LOH carried two point mutations, one on each allele. Although LOH was identified at one or more markers in 22 (59%) of 37 melanoma tumors corresponding to 20 (57%) of 35 individuals, only 11 tumors from 9 individuals [9 (26%) of 35] demonstrated LOH at D9S942 and D9S1748 the markers closest to CDKN2A. Of the remaining 11 tumors with LOH 9 demonstrated LOH at two or more contiguous markers either centromeric and/or telomeric to CDKN2A while retaining heterozygosity at several markers adjacent to CDKN2A. Multiplex PCR revealed one tumor carried a homozygous deletion extending from D9S1748 to the IFN-alpha locus. In the remaining eight tumors, multiplex PCR demonstrated that the observed heterozygosity was not attributable to homozygous deletion and stromal contamination at D9S1748, D9S942, or D9S974, as measured by comparative amplification strengths, which indicates that retention of heterozygosity with flanking LOH does not always indicate a homozygous deletion. This report supports the conclusions of previous studies that a least two TSGs involved in melanoma development in addition to CDKN2A may reside on chromosome 9p.

PTEN inactivation is rare in melanoma tumours but occurs frequently in melanoma cell lines

Deletions detected in cytogenetic and loss of heterozygosity (LOH) studies indicate that at least one tumour suppressor gene maps to the long arm of chromosome 10. Previous deletion mapping studies have observed LOH on 10q in about 30% of melanomas analysed. The PTEN gene, mapping to chromosome band 10q23.3, encodes a protein with both lipid and protein phosphatase activity. Somatic mutations and deletions in have been detected in a variety of cell lines and tumours, including melanoma samples. We performed mutation analyses and extensive allelic loss studies to investigate the role this gene plays in melanoma pathogenesis. We found that a total of 34 out of 57 (60%) melanoma cell lines carried hemizygous deletions of chromosome 10q encompassing the PTEN locus. A further three cell lines carried smaller deletions excluding PTEN. Inactivation of both PTEN alleles by exon-specific homozygous deletion or mutation was observed in 13 out of 57 (23%) melanoma cell lines. The mutation spectrum observed does not indicate an important role for ultraviolet radiation in the genesis of these mutations, and evidence from three cell lines supports the acquisition of PTEN aberrations in culture. Ten out of 49 (20%) matched melanoma tumour/normal samples harboured hemizygous deletions of either the whole chromosome or most of the long arm. Mutations within were detected in only one of the 10 tumours demonstrating LOH at 10q23 that were analysed. These results suggest that PTEN inactivation may be important for the propagation of melanoma cells in culture, and that another chromosome 10 tumour suppressor gene may be important for melanoma pathogenesis.

Deletion mapping suggests that the 1p22 melanoma susceptibility gene is a tumor suppressor localized to a 9-Mb interval

Loss of the short arm of chromosome 1 is frequently observed in many tumor types, including melanoma. We recently localized a third melanoma susceptibility locus to chromosome band 1p22. Critical recombinants in linked families localized the gene to a 15-Mb region between D1S430 and D1S2664. To map the locus more finely we have performed studies to assess allelic loss across the region in a panel of melanomas from 1p22-linked families, sporadic melanomas, and melanoma cell lines. Eighty percent of familial melanomas exhibited loss of heterozygosity (LOH) within the region, with a smallest region of overlapping deletions (SRO) of 9 Mb between D1S207 and D1S435. This high frequency of LOH makes it very likely that the susceptibility locus is a tumor suppressor. In sporadic tumors, four SROs were defined. SRO1 and SRO2 map within the critical recombinant and familial tumor region, indicating that one or the other is likely to harbor the susceptibility gene. However, SRO3 may also be significant because it overlaps with the markers with the highest 2-point LOD score (D1S2776), part of the linkage recombinant region, and the critical region defined in mesothelioma. The candidate genes PRKCL2 and GTF2B, within SRO2, and TGFBR3, CDC7, and EVI5, in a broad region encompassing SRO3, were screened in 1p22-linked melanoma kindreds, but no coding mutations were detected. Allelic loss in melanoma cell lines was significantly less frequent than in fresh tumors, indicating that this gene may not be involved late in progression, such as in overriding cellular senescence, necessary for the propagation of melanoma cells in culture.

Mapping the language of science and science teaching practices : a case study of early childhood school science

Concerns raised in educational reports about school science in terms of students. outcomes and attitudes, as well as science teaching practices prompted investigation into science learning and teaching practices at the foundational level of school science. Without science content and process knowledge, understanding issues of modern society and active participation in decision-making is difficult. This study contended that a focus on the development of the language of science could enable learners to engage more effectively in learning science and enhance their interest and attitudes towards science. Furthermore, it argued that explicit teaching practices where science language is modelled and scaffolded would facilitate the learning of science by young children at the beginning of their formal schooling. This study aimed to investigate science language development at the foundational level of school science learning in the preparatory-school with students aged five and six years. It focussed on the language of science and science teaching practices in early childhood. In particular, the study focussed on the capacity for young students to engage with and understand science language. Previous research suggests that students have difficulty with the language of science most likely because of the complexities and ambiguities of science language. Furthermore, literature indicates that tensions transpire between traditional science teaching practices and accepted early childhood teaching practices. This contention prompted investigation into means and models of pedagogy for learning foundational science language, knowledge and processes in early childhood. This study was positioned within qualitative assumptions of research and reported via descriptive case study. It was located in a preparatory-school classroom with the class teacher, teacher-aide, and nineteen students aged four and five years who participated with the researcher in the study. Basil Bernstein.s pedagogical theory coupled with Halliday.s Systemic Functional Linguistics (SFL) framed an examination of science pedagogical practices for early childhood science learning. Students. science learning outcomes were gauged by focussing a Hallydayan lens on their oral and reflective language during 12 science-focussed episodes of teaching. Data were collected throughout the 12 episodes. Data included video and audio-taped science activities, student artefacts, journal and anecdotal records, semi-structured interviews and photographs. Data were analysed according to Bernstein.s visible and invisible pedagogies and performance and competence models. Additionally, Halliday.s SFL provided the resource to examine teacher and student language to determine teacher/student interpersonal relationships as well as specialised science and everyday language used in teacher and student science talk. Their analysis established the socio-linguistic characteristics that promoted science competencies in young children. An analysis of the data identified those teaching practices that facilitate young children.s acquisition of science meanings. Positive indications for modelling science language and science text types to young children have emerged. Teaching within the studied setting diverged from perceived notions of common early childhood practices and the benefits of dynamic shifting pedagogies were validated. Significantly, young students demonstrated use of particular specialised components of school-science language in terms of science language features and vocabulary. As well, their use of language demonstrated the students. knowledge of science concepts, processes and text types. The young students made sense of science phenomena through their incorporation of a variety of science language and text-types in explanations during both teacher-directed and independent situations. The study informs early childhood science practices as well as practices for foundational school science teaching and learning. It has exposed implications for science education policy, curriculum and practices. It supports other findings in relation to the capabilities of young students. The study contributes to Systemic Functional Linguistic theory through the development of a specific resource to determine the technicality of teacher language used in teaching young students. Furthermore, the study contributes to methodology practices relating to Bernsteinian theoretical perspectives and has demonstrated new ways of depicting and reporting teaching practices. It provides an analytical tool which couples Bernsteinian and Hallidayan theoretical perspectives. Ultimately, it defines directions for further research in terms of foundation science language learning, ongoing learning of the language of science and learning science, science teaching and learning practices, specifically in foundational school science, and relationships between home and school science language experiences.

Hunters & gatherers : strategies for curriculum mapping and data collection for assurance of learning

Assurance of learning is a predominant feature in both quality enhancement and assurance in higher education. Assurance of learning is a process that articulates explicit program outcomes and standards, and systematically gathers evidence to determine the extent to which performance matches expectations. Benefits accrue to the institution through the systematic assessment of whole of program goals. Data may be used for continuous improvement, program development, and to inform external accreditation and evaluation bodies. Recent developments, including the introduction of the Tertiary Education and Quality Standards Agency (TEQSA) will require universities to review the methods they use to assure learning outcomes. This project investigates two critical elements of assurance of learning: 1. the mapping of graduate attributes throughout a program; and 2. the collection of assurance of learning data. An audit was conducted with 25 of the 39 Business Schools in Australian universities to identify current methods of mapping graduate attributes and for collecting assurance of learning data across degree programs, as well as a review of the key challenges faced in these areas. Our findings indicate that external drivers like professional body accreditation (for example: Association to Advance Collegiate Schools of Business (AACSB)) and TEQSA are important motivators for assuring learning, and those who were undertaking AACSB accreditation had more robust assurance of learning systems in place. It was reassuring to see that the majority of institutions (96%) had adopted an embedding approach to assuring learning rather than opting for independent standardised testing. The main challenges that were evident were the development of sustainable processes that were not considered a burden to academic staff, and obtainment of academic buy in to the benefits of assuring learning per se rather than assurance of learning being seen as a tick box exercise. This cultural change is the real challenge in assurance of learning practice.

Mapping resilience : A framework for changing cities

Urban centres base their resilience on the ability to evolve and adapt as needed throughout their life. Although constantly developing, changing and subsuming nature for its needs, the current age of environmental awareness requires that cities progress in a more conscious and considered way. While they have become the dominant form of human habitation, there now exists a need to integrate 'green' solutions into urban centres to address social, physical and environmental wellbeing. The means of implementing the vast array of possible solutions without negative impacts is not clear; cities are complex systems, layering meaning, history and cultural memory ‐ they are a manifestation of shared cultural values, and as such, they do not allow a tabula rasa approach of 'blanket' solutions. All around us, cities are continuing to develop and change, and although their form is varied ‐ sprawling cities with density and sustainability problems; or collapsing cities with 'dead' centres and dilapidated districts – a common issue is the resilience of the local identity. The strength or resilience of cities lies in the elements which have become fixed points in the urban structure, giving character and identity to a shared urban experience. These elements need to be identified and either maintained or revitalised. Similarly, the identification of urban elements which can most viably be modified without compromising character and identity of place, will assist in making concrete contributions to increasing both the sustainability and experience of cities, making them more resilient. Through an examination of case studies, this paper suggests a framework to inform urban renewal assessing the widespread elements which generate an urban identity, beyond the traditional approach of heritage conservation for cultural or tourist purposes. The rapid contemporary alteration of urban structures requires an innovative methodology which satisfies on one side the need of new sustainable performances and, on the other, the resilience of the local character.

How long is a tweet? Mapping dynamic conversation networks on Twitter using Gawk and Gephi

Twitter is now well established as the world’s second most important social media platform, after Facebook. Its 140-character updates are designed for brief messaging, and its network structures are kept relatively flat and simple: messages from users are either public and visible to all (even to unregistered visitors using the Twitter website), or private and visible only to approved ‘followers’ of the sender; there are no more complex definitions of degrees of connection (family, friends, friends of friends) as they are available in other social networks. Over time, Twitter users have developed simple, but effective mechanisms for working around these limitations: ‘#hashtags’, which enable the manual or automatic collation of all tweets containing the same #hashtag, as well allowing users to subscribe to content feeds that contain only those tweets which feature specific #hashtags; and ‘@replies’, which allow senders to direct public messages even to users whom they do not already follow. This paper documents a methodology for extracting public Twitter activity data around specific #hashtags, and for processing these data in order to analyse and visualize the @reply networks existing between participating users – both overall, as a static network, and over time, to highlight the dynamic structure of @reply conversations. Such visualizations enable us to highlight the shifting roles played by individual participants, as well as the response of the overall #hashtag community to new stimuli – such as the entry of new participants or the availability of new information. Over longer timeframes, it is also possible to identify different phases in the overall discussion, or the formation of distinct clusters of preferentially interacting participants.

Towards lifelong navigation and mapping in an office environment

This paper addresses the challenge of developing robots that map and navigate autonomously in real world, dynamic environments throughout the robot’s entire lifetime – the problem of lifelong navigation. Static mapping algorithms can produce highly accurate maps, but have found few applications in real environments that are in constant flux. Environments change in many ways: both rapidly and gradually, transiently and permanently, geometrically and in appearance. This paper demonstrates a biologically inspired navigation algorithm, RatSLAM, that uses principles found in rodent neural circuits. The algorithm is demonstrated in an office delivery challenge where the robot was required to perform mock deliveries to goal locations in two different buildings. The robot successfully completed 1177 out of 1178 navigation trials over 37 hours of around the clock operation spread over 11 days.

Outdoor simultaneous localisation and mapping using RatSLAM

In this paper an existing method for indoor Simultaneous Localisation and Mapping (SLAM) is extended to operate in large outdoor environments using an omnidirectional camera as its principal external sensor. The method, RatSLAM, is based upon computational models of the area in the rat brain that maintains the rodent’s idea of its position in the world. The system uses the visual appearance of different locations to build hybrid spatial-topological maps of places it has experienced that facilitate relocalisation and path planning. A large dataset was acquired from a dynamic campus environment and used to verify the system’s ability to construct representations of the world and simultaneously use these representations to maintain localisation.

Mapping intermedia news flows : topical discussions in the Australian and French political blogospheres

The growth of technologies and tools branded as =new media‘ or =Web 2.0‘ has sparked much discussion about the internet and its place in all facets of social life. Such debate includes the potential for blogs and citizen journalism projects to replace or alter journalism and mainstream media practices. However, while the journalism-blog dynamic has attracted the most attention, the actual work of political bloggers, the roles they play in the mediasphere and the resources they use, has been comparatively ignored. This project will look at political blogging in Australia and France - sites commenting on or promoting political events and ideas, and run by citizens, politicians, and journalists alike. In doing so, the structure of networks formed by bloggers and the nature of communication within political blogospheres will be examined. Previous studies of political blogging around the world have focussed on individual nations, finding that in some cases the networks are divided between different political ideologies. By comparing two countries with different political representation (two-party dominated system vs. a wider political spectrum), this study will determine the structure of these political blogospheres, and correlate these structures with the political environment in which they are situated. The thesis adapts concepts from communication and media theories, including framing, agenda setting, and opinion leaders, to examine the work of political bloggers and their place within the mediasphere. As well as developing a hybrid theoretical base for research into blogs and other online communication, the project outlines new methodologies for carrying out studies of online activity through the analysis of several topical networks within the wider activity collected for this project. The project draws on hyperlink and textual data collected from a sample of Australian and French blogs between January and August 2009. From this data, the thesis provides an overview of =everyday‘ political blogging, showing posting patterns over several months of activity, away from national elections and their associated campaigns. However, while other work in this field has looked solely at cumulative networks, treating collected data as a static network, this project will also look at specific cases to see how the blogospheres change with time and topics of discussion. Three case studies are used within the thesis to examine how blogs cover politics, featuring an international political event (the Obama inauguration), and local political topics (the opposition to the =Création et Internet‘, or HADOPI, law in France, the =Utegate‘ scandal in Australia). By using a mixture of qualitative and quantitative methods, the study analyses data collected from a population of sites from both countries, looking at their linking patterns, relationship with mainstream media, and topics of interest. This project will subsequently help to further develop methodologies in this field and provide new and detailed information on both online networks and internet-based political communication in Australia and France.

Mapping Australia's philanthropic investment in women and girls

The Australian Women Donors Network (Women Donors) partnered the Australian Centre for Philanthropy and Nonprofit Studies (ACPNS) at QUT to conduct this research. No studies exist on the size or sources of philanthropic giving in Australia directed intentionally towards the needs of women and girls. The survey aims to fill this knowledge gap and create a baseline for understanding trends and views in this area. Because the survey treads some new ground, its findings raise questions as well as giving answers. Encouragingly, 100 people from across the philanthropy spectrum completed the survey, embracing 41 individual donors and other respondents from various foundation types. Given the population difference, this response compares well with the 145 respondents to the USA-based Foundation Center’s 2009 European study (reported in 2011). The survey was designed for givers generally, not just those involved in giving to women and girls specifically. It is possible, though, that people with an interest in funding this area were more likely to participate. This potential oversampling may inflate the figures on funding women and girls to some degree. Also, because the population size of Australian philanthropists is unknown, no claims can be made that this information is generalizable to all Australian funders. Nonetheless, some patterns and themes emerge from the 100 responses.

Mapping of shallow coastal groundwaters, their hydrology and environmental geochemistry : Pumicestone catchment, Southeast Queensland

Blooms of the toxic cyanobacterium majuscula Lyngbya in the coastal waters of southeast Queensland have caused adverse impacts on both environmental health and human health, and on local economies such as fishing and tourism. A number of studies have confirmed that the main limiting nutrients (“nutrients of concern”) that contribute to these blooms area Fe, DOC, N, P and also pH. This study is conducted to establish the distribution of these parameters in a typical southeast Queensland coastal setting. The study maps the geochemistry of shallow groundwater in the mainland Pumicestone catchment with an emphasis on the nutrients of concern to understand how these nutrients relate to aquifer materials, landuse and anthropogenic activities. The results of the study form a GIS information layer which will be incorporated into a larger GIS model being produced by Queensland Department of Environment and Resource Management (DERM) to support landuse management to avoid/minimize blooms of Lyngbya in Moreton Bay, southeast Queensland, and other similar settings. A total of 38 boreholes were established in the mainland Pumicestone region and four sampling rounds of groundwater carried out in both dry and wet conditions. These groundwater samples were measured in the field for physico-chemical parameters, and in the laboratory analyses for the nutrients of concern, and other major and minor ions. Aquifer materials were confirmed using the Geological Survey of Queensland digital geology map, and geomaterials were assigned to seven categories which are A (sands), B (silts, sandy silts), C (estuarine mud, silts), D (humid soils), E (alluvium), F (sandstone) and G (other bedrock). The results of the water chemistry were examined by use of the software package AquaChem/AqQA, and divided into six groundwater groups, based on groundwater chemical types and location of boreholes. The type of aquifer material and location, and proximity to waterways was found to be important because they affected physico-chemical properties and concentrations of nutrients of concern and dissolved ions. The analytical results showed that iron concentrations of shallow groundwaters were high due to acid sulfate soils, and also mud and silt, but were lower in sand materials. DOC concentrations of these shallow groundwaters in the sand material were high probably due to rapid infiltration. In addition, DOC concentrations in some boreholes were high because they were installed in organic rich wetlands. The pH values of boreholes were from acidic to near neutral; some boreholes with pH values were low (< 4), showing acid sulfate soils in these boreholes. Concentrations of total nitrogen and total phosphorus of groundwaters were generally low, and the main causes of elevated concentrations of total nitrogen and total phosphorus are largely due to animal and human wastes and tend to be found in localized source areas. Comparison of the relative percentage of nitrogen species (NH3/NH4< Org-N, NO3-N and NO2-N) demonstrated that they could be related to sources such as animal waste, residential and agricultural fertilizers, forest and vegetation, mixed residents and farms, and variable setting and vegetation covers. Total concentrations of dissolved ions in sampling round 3 (dry period) were higher than those in sampling round 2 (wet period) due to both evaporation of groundwater in the dry period and the dilution of rainfall in the wet period. This showed that the highest concentrations of nutrients of concern were due to acid sulfate soils, aquifer materials, landuse and anthropogenic activities and were typically in aquifer materials of E (alluvium) and C (estuarine muds) and locations of Burpengary, Caboolture, and Glass Mountain catchments.