A high-throughput panel for identifying clinically relevant mutation profiles in melanoma

Success with molecular-based targeted drugs in the treatment of cancer has ignited extensive research efforts within the field of personalized therapeutics. However, successful application of such therapies is dependent on the presence or absence of mutations within the patient's tumor that can confer clinical efficacy or drug resistance. Building on these findings, we developed a high-throughput mutation panel for the identification of frequently occurring and clinically relevant mutations in melanoma. An extensive literature search and interrogation of the Catalogue of Somatic Mutations in Cancer database identified more than 1,000 melanoma mutations. Applying a filtering strategy to focus on mutations amenable to the development of targeted drugs, we initially screened 120 known mutations in 271 samples using the Sequenom MassARRAY system. A total of 252 mutations were detected in 17 genes, the highest frequency occurred in BRAF (n = 154, 57%), NRAS (n = 55, 20%), CDK4 (n = 8, 3%), PTK2B (n = 7, 2.5%), and ERBB4 (n = 5, 2%). Based on this initial discovery screen, a total of 46 assays interrogating 39 mutations in 20 genes were designed to develop a melanoma-specific panel. These assays were distributed in multiplexes over 8 wells using strict assay design parameters optimized for sensitive mutation detection. The final melanoma-specific mutation panel is a cost effective, sensitive, high-throughput approach for identifying mutations of clinical relevance to molecular-based therapeutics for the treatment of melanoma. When used in a clinical research setting, the panel may rapidly and accurately identify potentially effective treatment strategies using novel or existing molecularly targeted drugs

Identification of TFG (TRK-fused gene) as a putative metastatic melanoma tumor suppressor gene

High density SNP arrays can be used to identify DNA copy number changes in tumors such as homozygous deletions of tumor suppressor genes and focal amplifications of oncogenes. Illumina Human CNV370 Bead chip arrays were used to assess the genome for unbalanced chromosomal events occurring in 39 cell lines derived from stage III metastatic melanomas. A number of genes previously recognized to have an important role in the development and progression of melanoma were identified including homozygous deletions of CDKN2A (13 of 39 samples), CDKN2B (10 of 39), PTEN (3 of 39), PTPRD (3 of 39), TP53 (1 of 39), and amplifications of CCND1 (2 of 39), MITF (2 of 39), MDM2 (1 of 39), and NRAS (1 of 39). In addition, a number of focal homozygous deletions potentially targeting novel melanoma tumor suppressor genes were identified. Because of their likely functional significance for melanoma progression, FAS, CH25H, BMPR1A, ACTA2, and TFG were investigated in a larger cohort of melanomas through sequencing. Nonsynonymous mutations were identified in BMPR1A (1 of 43), ACTA2 (3 of 43), and TFG (5 of 103). A number of potentially important mutation events occurred in TFG including the identification of a mini mutation ‘‘hotspot’’ at amino acid residue 380 (P380S and P380L) and the presence of multiple mutations in two melanomas. Mutations in TFG may have important clinical relevance for current therapeutic strategies to treat metastatic melanoma.

How can Australia sustain middle school education?

Middle school is a crucial area of education where adolescents experiencing physiological and psychological changes, and require expert guidance. As more research evidence is provided about adolescent learning, teachers are considered pivotal to adolescents’ educational development. Reform measures need to be targeted at the inservice and preservice teacher levels. This quantitative study employs a 40-item, five part Likert scale survey to understand preservice teachers’ (n = 142) perceptions of their confidence to teach in a middle school at the conclusion of their tertiary education. The survey instrument was developed from the literature, with connections to the Queensland College of Teachers' professional standards. Results indicated that they perceived themselves as capable of creating a positive classroom environment with seven items greater than 80%, except with behaviour management (< 80% for two items), and they considered their pedagogical knowledge to be adequate (i.e., 7 out of 8 items > 84%). Items associated with implementing a middle school curriculum had varied responses (e.g., implementing literacy and numeracy were 74%, while implementing learning with real world connections was 91%). This information may assist coursework designers. For example, if a significant percentages of preservice teachers indicate that they believe they were not well prepared for assessment and reporting at the middle school level, then course designers can target these areas more effectively.

Enhancing teacher education : the School-Community Intergrated Learning (SCIL) pathway

National Australian reviews advocate exploring new models for preservice teacher education. This study investigates the outcomes of the School-Community Integrated Learning (SCIL) pathway as a model for advancing preservice teachers’ understandings of teaching. Thirty-two final-year preservice teachers were surveyed with extended written responses on how the SCIL pathway advanced their understandings of teaching. Results indicated 100% agreement on 6 of the 27 survey items. Indeed, 78% or more preservice teachers agreed that they had a range of experiences across the five categories (i.e., personal-professional skill development, understandings of system requirements, teaching practices, student behaviour and reflective practices). Extended responses suggested they had developed understandings around setting up classrooms, whole school planning processes with professional development, the allocation of teacher responsibilities (e.g., playground duties), parent-teacher interviews, diagnostic testing for literacy and numeracy, commencing running records of students’ assessment results, and the development of relationships (students, teachers and parents). Although a longitudinal study is required to determine long-term effects, the SCIL pathway may be viewed as a positive step towards preparing final-year preservice teachers for their first year as fully-fledged teachers.

The need for legislative reform of the privity doctrine in commercial contracts in Malaysia : a comparative analysis

This thesis commences with the proposition that the first limb of the doctrine of privity causes injustice to third party beneficiaries in Malaysia, particularly in commercial contracts. The doctrine of privity has been the subject of criticism by the judiciary and academic commentators in common law jurisdictions, mainly directed at the first limb of the doctrine, whereby only parties to a contract can sue and be sued. The first limb prevents a third party from enforcing benefits conferred on them by those contracts thereby resulting in third parties suffering loss and injustice to those parties. In several common law countries, such as England, Australia, New Zealand and Singapore, legislative reform of the doctrine has occurred. The legislative reform has abrogated to a significant extent the doctrine of privity in commercial contracts. Malaysia is a common law country, where the doctrine of privity is still applied to contracts. An analysis of Malaysian case law demonstrates that the most affected third party beneficiaries are those seeking to enforce insurance and construction contracts. While a small number of other third parties to commercial contracts, such as agreements to pay for work done, sale and purchase agreements and tenancy agreements are also affected, the detriment is not as significant. As a consequence, this thesis focuses primarily on the impact of the doctrine of privity on commercial contracts in the areas of insurance and construction in Malaysia The thesis aims to recommend appropriate reforms to address the injustices arising from the privity doctrine for third parties seeking to obtain the benefit of insurance and construction contracts, which may also benefit third parties to other types of commercial contracts. While the Malaysian insurance, consumer protection, negotiable instruments and agency laws allow third party beneficiaries to enforce benefits in contracts, the rights are found to be inadequate. As not all third parties seeking to enforce an insurance or construction contract can rely upon the legislation, the injustice arising from the doctrine of privity remains and needs to be addressed. To achieve this aim, a comparative analysis of the rights of third party beneficiaries under insurance and construction contracts in Malaysia, Australia and England is undertaken. The results of the analysis are used to identify appropriate elements for a legislative framework guided by the three essential criteria for effective law reform developed in the thesis. The three criteria are certainty, public interest and justice. The thesis recommends first the enactment of general legislation applicable to all commercial contracts including insurance contracts. Secondly, the thesis recommends specific targeted legislation to address the injustice faced by third party beneficiaries in construction contracts.

Beyond compliance : project on an integrated systems approach for pest risk management in South East Asia

The Beyond Compliance project, which began in July 2011 with funding from the Standards and Trade Development Facility for 2 years, aims to enhance competency and confidence in the South East Asian sub-region by applying a Systems Approach for pest risk management. The Systems Approach involves the use of integrated measures, at least two of which are independent, that cumulatively reduce the risk of introducing exotic pests through trade. Although useful in circumstances where single measures are inappropriate or unavailable, the Systems Approach is inherently more complicated than single-measure approaches, which may inhibit its uptake. The project methodology is to take prototype decision-support tools, such as Control Point-Bayesian Networks (CP-BN), developed in recent plant health initiatives in other regions, including the European PRATIQUE project, and to refine them within this sub-regional context. Case studies of high-priority potential agricultural trade will be conducted by National Plant Protection Organizations of participating South East Asian countries in trials of the tools, before further modifications. Longer term outcomes may include: more robust pest risk management in the region (for exports and imports); greater inclusion of stakeholders in development of pest risk management plans; increased confidence in trade negotiations; and new opportunities for trade.

Mastery Motivation in Children with Down Syndrome : Promoting and Sustaining Interest in Learning

Motivation is central to children’s learning. Without persistent effort, especially in the face of failure, and an eagerness to engage in challenging tasks, individuals are unlikely to learn as effectively as they might. Because of their cognitive impairments, children with Down syndrome will almost certainly have difficulties with learning. These difficulties will be ameliorated somewhat by strong engagement with learning activities whereas problems with motivation are likely to further jeopardise their academic progress as well as potentially limiting achievements in other areas of life. In this chapter we begin with a general overview of motivation. Using the framework of mastery motivation, we review the relatively small amount of research about children with Down syndrome. We identify the individual characteristics and features of children’s environments that are likely to be related to lower or higher levels of mastery motivation. In the final section, we consider implications for educators and then draw together the findings to provide a set of recommendations for future research.

Learning about being effective mentors : professional learning communities and mentoring

This study aimed to explore experienced mentors’ understandings about professional learning communities (PLCs), mentoring and leadership. This research analyses audio-taped transcripts and written responses from 27 experienced mentors who operate in varied roles (e.g., university academics, school executives, teachers, learning support personnel). Findings indicated that PLCs can provide professional renewal for existing teachers and that mentoring within PLCs can further advance knowledge about effective practices. PLCs can include other staff members and key stakeholders (e.g., preservice teachers, teacher aides) who can contribute to the learning within the group. Mentoring and PLCs can be cost-effective strategic levers for advancing professional knowledge.

Evaluation of the alkaline comet assay and urinary 3-methyladenine excretion for monitoring DNA damage in melanoma patients treated with dacarbazine and tamoxifen

Purpose: To develop, using dacarbazine as a model, reliable techniques for measuring DNA damage and repair as pharmacodynamic endpoints for patients receiving chemotherapy. Methods: A group of 39 patients with malignant melanoma were treated with dacarbazine 1 g/m2 i.v. every 21 days. Tamoxifen 20 mg daily was commenced 24 h after the first infusion and continued until 3 weeks after the last cycle of chemotherapy. DNA strand breaks formed during dacarbazine-induced DNA damage and repair were measured in individual cells by the alkaline comet assay. DNA methyl adducts were quantified by measuring urinary 3-methyladenine (3-MeA) excretion using immunoaffinity ELISA. Venous blood was taken on cycles 1 and 2 for separation of peripheral blood lymphocytes (PBLs) for measurement of DNA strand breaks. Results: Wide interpatient variation in PBL DNA strand breaks occurred following chemotherapy, with a peak at 4 h (median 26.6 h, interquartile range 14.75- 40.5 h) and incomplete repair by 24 h. Similarly, there was a range of 3-MeA excretion with peak levels 4-10 h after chemotherapy (median 33 nmol/h, interquartile range 20.448.65 nmol/h). Peak 3-MeA excretion was positively correlated with DNA strand breaks at 4 h (Spearman's correlation coefficient, r = 0.39, P = 0.036) and 24 h (r = 0.46, P = 0.01). Drug-induced emesis correlated with PBL DNA strand breaks (Mann Whitney U-test, P = 0.03) but not with peak 3-MeA excretion. Conclusions: DNA damage and repair following cytotoxic chemotherapy can be measured in vivo by the alkaline comet assay and by urinary 3-MeA excretion in patients receiving chemotherapy.

Utilising hospital data to inform product safety prioritisation : the application of RAPEX severity rankings in ICD-coded burn data

Background The implementation of the Australian Consumer Law in 2011 highlighted the need for better use of injury data to improve the effectiveness and responsiveness of product safety (PS) initiatives. In the PS system, resources are allocated to different priority issues using risk assessment tools. The rapid exchange of information (RAPEX) tool to prioritise hazards, developed by the European Commission, is currently being adopted in Australia. Injury data is required as a basic input to the RAPEX tool in the risk assessment process. One of the challenges in utilising injury data in the PS system is the complexity of translating detailed clinical coded data into broad categories such as those used in the RAPEX tool. Aims This study aims to translate hospital burns data into a simplified format by mapping the International Statistical Classification of Disease and Related Health Problems (Tenth Revision) Australian Modification (ICD-10-AM) burn codes into RAPEX severity rankings, using these rankings to identify priority areas in childhood product-related burns data. Methods ICD-10-AM burn codes were mapped into four levels of severity using the RAPEX guide table by assigning rankings from 1-4, in order of increasing severity. RAPEX rankings were determined by the thickness and surface area of the burn (BSA) with information extracted from the fourth character of T20-T30 codes for burn thickness, and the fourth and fifth characters of T31 codes for the BSA. Following the mapping process, secondary data analysis of 2008-2010 Queensland Hospital Admitted Patient Data Collection (QHAPDC) paediatric data was conducted to identify priority areas in product-related burns. Results The application of RAPEX rankings in QHAPDC burn data showed approximately 70% of paediatric burns in Queensland hospitals were categorised under RAPEX levels 1 and 2, 25% under RAPEX 3 and 4, with the remaining 5% unclassifiable. In the PS system, prioritisations are made to issues categorised under RAPEX levels 3 and 4. Analysis of external cause codes within these levels showed that flammable materials (for children aged 10-15yo) and hot substances (for children aged <2yo) were the most frequently identified products. Discussion and conclusions The mapping of ICD-10-AM burn codes into RAPEX rankings showed a favourable degree of compatibility between both classification systems, suggesting that ICD-10-AM coded burn data can be simplified to more effectively support PS initiatives. Additionally, the secondary data analysis showed that only 25% of all admitted burn cases in Queensland were severe enough to trigger a PS response.

Understanding theory of mind in children who are deaf

Research on theory of mind began in the context of determining whether chimpanzees are aware that individuals experience cognitive and emotional states. More recently, this research has involved various groups of children and various tasks, including the false belief task. Based almost exclusively on that paradigm, investigators have concluded that although ``normal'' hearing children develop theory of mind by age 5, children who are autistic or deaf do not do so until much later, perhaps not until their teenage years. The present study explored theory of mind by examining stories told by children who are deaf and hearing (age 9±15 years) for statements ascribing behaviour-relevant states of mind to themselves and others. Both groups produced such attributions, although there were reliable differences between them. Results are discussed in terms of the cognitive abilities assumed to underlie false belief and narrative paradigms and the implications of attributing theory of mind solely on the basis of performance on the false belief task.

Utilising hospital data to inform product safety prioritisation : the application of RAPEX severity rankings in ICD-coded Burn Data

Background The implementation of the Australian Consumer Law in 2011 highlighted the need for better use of injury data to improve the effectiveness and responsiveness of product safety (PS) initiatives. In the PS system, resources are allocated to different priority issues using risk assessment tools. The rapid exchange of information (RAPEX) tool to prioritise hazards, developed by the European Commission, is currently being adopted in Australia. Injury data is required as a basic input to the RAPEX tool in the risk assessment process. One of the challenges in utilising injury data in the PS system is the complexity of translating detailed clinical coded data into broad categories such as those used in the RAPEX tool. Aims This study aims to translate hospital burns data into a simplified format by mapping the International Statistical Classification of Disease and Related Health Problems (Tenth Revision) Australian Modification (ICD-10-AM) burn codes into RAPEX severity rankings, using these rankings to identify priority areas in childhood product-related burns data. Methods ICD-10-AM burn codes were mapped into four levels of severity using the RAPEX guide table by assigning rankings from 1-4, in order of increasing severity. RAPEX rankings were determined by the thickness and surface area of the burn (BSA) with information extracted from the fourth character of T20-T30 codes for burn thickness, and the fourth and fifth characters of T31 codes for the BSA. Following the mapping process, secondary data analysis of 2008-2010 Queensland Hospital Admitted Patient Data Collection (QHAPDC) paediatric data was conducted to identify priority areas in product-related burns. Results The application of RAPEX rankings in QHAPDC burn data showed approximately 70% of paediatric burns in Queensland hospitals were categorised under RAPEX levels 1 and 2, 25% under RAPEX 3 and 4, with the remaining 5% unclassifiable. In the PS system, prioritisations are made to issues categorised under RAPEX levels 3 and 4. Analysis of external cause codes within these levels showed that flammable materials (for children aged 10-15yo) and hot substances (for children aged <2yo) were the most frequently identified products. Discussion and conclusions The mapping of ICD-10-AM burn codes into RAPEX rankings showed a favourable degree of compatibility between both classification systems, suggesting that ICD-10-AM coded burn data can be simplified to more effectively support PS initiatives. Additionally, the secondary data analysis showed that only 25% of all admitted burn cases in Queensland were severe enough to trigger a PS response.

A review of sedation scales for the cardiac catheterization laboratory

Sedation scales have the potential to facilitate effective procedural sedation and analgesia in the cardiac catheterization laboratory (CCL). For this potential to become realised, a scale that is suitable for use in the CCL either needs to be identified or developed. To identify sedation scales, a review of Medline and CINHAL was conducted. One sedation scale for the CCL, the NASPE SED, and 15 Intensive Care Unit (ICU) scales met the inclusion and exclusion criteria. Analysis of the scale’s item structures and psychometric properties was then performed. None of these scales were deemed suitable for use in the CCL. As such, further research is required to develop a new scale. The new scale should consist of more than one item because it will be the most effective for tracking the patient’s response to medications. Specific tests required to conduct a rigorous evaluation of the new scale’s psychometric properties are outlined in this paper.