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

Expression and prognostic significance of a panel of tissue hypoxia markers in head-and-neck squamous cell carcinomas

Purpose: To investigate the expression pattern of hypoxia-induced proteins identified as being involved in malignant progression of head-and-neck squamous cell carcinoma (HNSCC) and to determine their relationship to tumor pO 2 and prognosis. Methods and Materials: We performed immunohistochemical staining of hypoxia-induced proteins (carbonic anhydrase IX [CA IX], BNIP3L, connective tissue growth factor, osteopontin, ephrin A1, hypoxia inducible gene-2, dihydrofolate reductase, galectin-1, IκB kinase β, and lysyl oxidase) on tumor tissue arrays of 101 HNSCC patients with pretreatment pO 2 measurements. Analysis of variance and Fisher's exact tests were used to evaluate the relationship between marker expression, tumor pO 2, and CA IX staining. Cox proportional hazard model and log-rank tests were used to determine the relationship between markers and prognosis. Results: Osteopontin expression correlated with tumor pO 2 (Eppendorf measurements) (p = 0.04). However, there was a strong correlation between lysyl oxidase, ephrin A1, and galectin-1 and CA IX staining. These markers also predicted for cancer-specific survival and overall survival on univariate analysis. A hypoxia score of 0-5 was assigned to each patient, on the basis of the presence of strong staining for these markers, whereby a higher score signifies increased marker expression. On multivariate analysis, increasing hypoxia score was an independent prognostic factor for cancer-specific survival (p = 0.015) and was borderline significant for overall survival (p = 0.057) when adjusted for other independent predictors of outcomes (hemoglobin and age). Conclusions: We identified a panel of hypoxia-related tissue markers that correlates with treatment outcomes in HNSCC. Validation of these markers will be needed to determine their utility in identifying patients for hypoxia-targeted therapy. © 2007 Elsevier Inc. All rights reserved.

Fiction as a form of change : a paper overview of a literature panel discussion

It is well established that literary work can promote insights that result in future change, whether on a personal or an institutional level. As Umberto Eco (1989) notes, the act of reading does not stop with the artist but continues into the work of communities. The papers delivered in this panel consider the regenerative role of literature within culture, arguing that the special properties of literature can convey an important sense of nature (Bateson 1973, Zapf 2008). These concepts are discussed in relation to writing about Australian flora and fauna. Using an ecocritical focus based on ideas about the relationship between literature and the environment the paper considers Australian works and the way in which literature enlivens this complex intersection between humans, animals and the environment. This engagement is investigated through three modes: the philosophical, the literary, and the practical. The novels discussed include Alexis Wright’s Carpentaria, Richard Flanagan’s Wanting, and Sonya Hartnett’s Forest, as well as a range of fictional and non-fictional works that describe the Blue Mountains region in New South Wales. The paper closes with a discussion of the role of story-telling as a way of introducing the public to specific environmental locations and issues.

Information systems success research : the “20-year update?” panel report from PACIS, 2011

This article summarizes a panel held at the 15th Pacific Asia Conference on Information Systems (PACIS) in Brisbane, Austrailia, in 2011. The panelists proposed a new research agenda for information systems success research. The DeLone and McLean IS Success Model has been one of the most influential models in Information Systems research. However, the nature of information systems continues to change. Information systems are increasingly implemented across layers of infrastructure and application architecture. The diffusion of information systems into many spheres of life means that information systems success needs to be considered in multiple contexts. Services play a much more prominent role in the economies of countries, making the “service” context of information systems increasingly important. Further, improved understandings of theory and measurement offer new opportunities for novel approaches and new research questions about information systems success.

Improving the detection of donations within the RHD negative blood donor panel which weakly express the RHD antigen

This project improved the detection and classification of very weakly expressed RhD variants in the Australian blood donor panel and contributed to the knowledge of anti-D reactivity patterns of RHD alleles that are undescribed. As such, the management of donations possessing these RHD alleles can be improved upon and the overall safety of transfusion medicine pertaining to the Rh blood group system will be increased. Future projects at ARCBS will be able to utilise the procedures developed in this project, thereby decreasing throughput time. The specificity of current testing will be improved and the need for outsourced RHD testing diminished.

Nanofabrication of single-crystalline flat-panel display microemitters : a plasma-building unit approach

This contribution is focused on plasma-enhanced chemical vapor deposition systems and their unique features that make them particularly attractive for nanofabrication of flat panel display microemitter arrays based on ordered patterns of single-crystalline carbon nanotip structures. The fundamentals of the plasma-based nanofabrication of carbon nanotips and some other important nanofilms and nanostructures are examined. Specific features, challenges, and potential benefits of using the plasma-based systems for relevant nanofabrication processes are analyzed within the framework of the "plasma-building unit" approach that builds up on extensive experimental data on plasma diagnostics and nanofilm/nanostructure characterization, and numerical simulation of the species composition in the ionized gas phase (multicomponent fluid models), ion dynamics and interaction with ordered carbon nanotip patterns, and ab initio computations of chemical structure of single crystalline carbon nanotips. This generic approach is also applicable for nanoscale assembly of various carbon nanostructures, semiconductor quantum dot structures, and nano-crystalline bioceramics. Special attention is paid to most efficient control strategies of the main plasma-generated building units both in the ionized gas phase and on nanostructured deposition surfaces. The issues of tailoring the reactive plasma environments and development of versatile plasma nanofabrication facilities are also discussed.

Protect or deter? : the expert panel on asylum seekers in Australia

In June 2012 Prime Minister Gillard appointed an Expert Panel on Asylum Seekers to provide advice on policy options 'to prevent asylum seekers rising their lives on dangerous boat journeys to Australia'. This article examines the establishment of that Committee against the backdrop of an increasing number of boat arrivals, of deaths at sea and the failure of Government policy responses to prevent them. It examines the recommendations of the Expert Panel and considers the punitive outcome of some of these recommendations including the 'no advantage' test. It evaluates Kevin Rudd's Regional Resettlement Arrangement with Papua New Guinea and concludes that Australian and regional initiatives need to focus on protection of asylum seekers, not deterrence or avoidance of international obligations

Australian patent enforcement : a proposal for an expert panel opinion

The Australian Government has been concerned “to find ways of making patent enforcement less of an issue” and to make it “cheaper, simpler and quicker to get fair and appropriate resolution for any dispute”. Major problems relating to patent enforcement in Australia have been identified as: the cost of legal proceedings; the lack of patent owners’ financial capacity to fund enforcement proceedings; delay; and uncertainty as to the outcome and lack of knowledge about the processes of enforcement. This paper considers some of the problems associated with patent enforcement in Australia and proposes an approach to patent litigation which is directed at alleviating some of the difficulties which have been identified. Specifically, it proposes a strategy designed to identify the parties’ risks at an early stage of patent litigation proceeding and facilitate an early resolution of the dispute.

A biomarker panel to discriminate between systemic inflammatory response syndrome and sepsis and sepsis severity

Introduction: In this study, we report on initial efforts to discover putative biomarkers for differential diagnosis of a systemic inflammatory response syndrome (SIRS) versus sepsis; and different stages of sepsis. In addition, we also investigated whether there are proteins that can discriminate between patients who survived sepsis from those who did not. Materials and Methods: Our study group consisted of 16 patients, of which 6 died and 10 survived. We daily measured 28 plasma proteins, for the whole stay of the patients in the ICU. Results: We observed that metalloproteinases and sE-selectin play a role in the distinction between SIRS and sepsis, and that IL-1, IP-10, sTNF-R2 and sFas appear to be indicative for the progression from sepsis to septic shock. A combined measurement of MMP-3, -10, IL-1, IP-10, sIL-2R, sFas, sTNF-R1, sRAGE, GM-CSF, IL-1 and Eotaxin allows for a good separation of patients that survived from those that died (mortality prediction with a sensitivity of 79% and specificity of 86%). Correlation analysis suggests a novel interaction between IL-1a and IP-10. Conclusion: The marker panel is ready to be verified in a validation study with or without therapeutic intervention.

A novel saliva-based microRNA biomarker panel to detect head and neck cancers

Background MicroRNAs (miRNAs) are known to play an important role in cancer development by post-transcriptionally affecting the expression of critical genes. The aims of this study were two-fold: (i) to develop a robust method to isolate miRNAs from small volumes of saliva and (ii) to develop a panel of saliva-based diagnostic biomarkers for the detection of head and neck squamous cell carcinoma (HNSCC). Methods Five differentially expressed miRNAs were selected from miScript™ miRNA microarray data generated using saliva from five HNSCC patients and five healthy controls. Their differential expression was subsequently confirmed by RT-qPCR using saliva samples from healthy controls (n = 56) and HNSCC patients (n = 56). These samples were divided into two different cohorts, i.e., a first confirmatory cohort (n = 21) and a second independent validation cohort (n = 35), to narrow down the miRNA diagnostic panel to three miRNAs: miR-9, miR-134 and miR-191. This diagnostic panel was independently validated using HNSCC miRNA expression data from The Cancer Genome Atlas (TCGA), encompassing 334 tumours and 39 adjacent normal tissues. Receiver operating characteristic (ROC) curve analysis was performed to assess the diagnostic capacity of the panel. Results On average 60 ng/μL miRNA was isolated from 200 μL of saliva. Overall a good correlation was observed between the microarray data and the RT-qPCR data. We found that miR-9 (P <0.0001), miR-134 (P <0.0001) and miR-191 (P <0.001) were differentially expressed between saliva from HNSCC patients and healthy controls, and that these miRNAs provided a good discriminative capacity with area under the curve (AUC) values of 0.85 (P <0.0001), 0.74 (P < 0.001) and 0.98 (P < 0.0001), respectively. In addition, we found that the salivary miRNA data showed a good correlation with the TCGA miRNA data, thereby providing an independent validation. Conclusions We show that we have developed a reliable method to isolate miRNAs from small volumes of saliva, and that the saliva-derived miRNAs miR-9, miR-134 and miR-191 may serve as novel biomarkers to reliably detect HNSCC. © 2014 International Society for Cellular Oncology.

Effects of microfinance on poverty reduction in Vietnam : a pseudo-panel data analysis

The development of microfinance in Vietnam since 1990s has coincided with a remarkable progress in poverty reduction. Numerous descriptive studies have illustrated that microfinance is an effective tool to eradicate poverty in Vietnam but evidence from quantitative studies is mixed. This study contributes to the literature by providing new evidence on the impact of microfinance to poverty reduction in Vietnam using the repeated cross - sectional data from the Vietnam Living Standard s Survey (VLSS) during period 1992 - 2010. Our results show that micro - loans contribute significantly to household consumption.

What roles do contemporaneous and cumulative incomes play in the income–child health gradient for young children? Evidence from an Australian Panel

The literature to date shows that children from poorer households tend to have worse health than their peers, and the gap between them grows with age. We investigate whether and how health shocks (as measured by the onset of chronic conditions) contribute to the income–child health gradient and whether the contemporaneous or cumulative effects of income play important mitigating roles. We exploit a rich panel dataset with three panel waves called the Longitudinal Study of Australian children. Given the availability of three waves of data, we are able to apply a range of econometric techniques (e.g. fixed and random effects) to control for unobserved heterogeneity. The paper makes several contributions to the extant literature. First, it shows that an apparent income gradient becomes relatively attenuated in our dataset when the cumulative and contemporaneous effects of household income are distinguished econometrically. Second, it demonstrates that the income–child health gradient becomes statistically insignificant when controlling for parental health and health-related behaviours or unobserved heterogeneity.

Feminism and art in 2013 : a panel discussion

Brisbane-based artist and Founding Co-Director of LEVEL artist run initiative Courtney Coombs reports on a one day forum about Feminism and Art held at LEVEL on International Womens Day 2013. LEVEL is focused on providing opportunities for female visual artists and generating dialogue around gender and arts practice. To listen to podcasts from the event visit http://www.ciprecinct.qut.edu.au/archive/2013/feminism-art.jsp

A novel approach to increasing inventory with the current panel: Increasing donation frequency by asking for a different blood product

BACKGROUND Ongoing shortages of blood products may be addressed through additional donations. However, donation frequency rates are typically lower than medically possible. This preliminary study aims to determine voluntary nonremunerated whole blood (WB) and plasmapheresis donors' willingness, and subsequent facilitators and barriers, to make additional donations of a different type. STUDY DESIGN AND METHODS Forty individual telephone interviews were conducted posing two additional donation pattern scenarios: first, making a single and, second, making multiple plasmapheresis donations between WB donations. Stratified purposive sampling was conducted for four samples varying in donation experience: no-plasma, new-to-both-WB-and-plasma, new-to-plasma, and plasma donors. Interviews were analyzed yielding excellent (κ values > 0.81) inter-rater reliability. RESULTS Facilitators were more endorsed than barriers for a single but not multiple plasmapheresis donation. More new-to-both donors (n = 5) were willing to make multiple plasma donations between WB donations than others (n = 1 each) and identified fewer barriers (n = 3) than those more experienced in donation (n = 8 no plasma, n = 10 new to both, n = 11 plasma). Donors in the plasma sample were concerned about the subsequent reduced time between plasma donations by adding WB donations (n = 3). The no-plasma and new-to-plasma donors were concerned about the time commitment required (n = 3). CONCLUSION Current donors are willing to add different product donations but donation history influences their willingness to change. Early introduction of multiple donation types, variation in inventory levels, and addressing barriers will provide blood collection agencies with a novel and cost-effective inventory management strategy.