Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the Lipooligosaccharide

Lipooligosaccharide (LOS) is a complex surface structure that is linked to many pathogenic properties of Acinetobacter baumannii. In A. baumannii, the genes responsible for the synthesis of the outer core (OC) component of the LOS are located between ilvE and aspS. The content of the OC locus is usually variable within a species, and examination of 6 complete and 227 draft A. baumannii genome sequences available in GenBank non-redundant and Whole Genome Shotgun databases revealed nine distinct new types, OCL4-OCL12, in addition to the three known ones. The twelve gene clusters fell into two distinct groups, designated Group A and Group B, based on similarities in the genes present. OCL6 (Group B) was unique in that it included genes for the synthesis of L-Rhamnosep. Genetic exchange of the different configurations between strains has occurred as some OC forms were found in several different sequence types (STs). OCL1 (Group A) was the most widely distributed being present in 18 STs, and OCL6 was found in 16 STs. Variation within clones was also observed, with more than one OC locus type found in the two globally disseminated clones, GC1 and GC2, that include the majority of multiply antibiotic resistant isolates. OCL1 was the most abundant gene cluster in both GC1 and GC2 genomes but GC1 isolates also carried OCL2, OCL3 or OCL5, and OCL3 was also present in GC2. As replacement of the OC locus in the major global clones indicates the presence of sub-lineages, a PCR typing scheme was developed to rapidly distinguish Group A and Group B types, and to distinguish the specific forms found in GC1 and GC2 isolates.

Differences in composition of symptom clusters between older and younger oncology patients

Context Older oncology patients have unique needs associated with the many physical, psychological,and social changes associated with the aging process. The mechanisms underpinning and the impact of these changes are not well understood. Identification of clusters of symptoms is one approach that has been used to elicit hypotheses about the biological and/or psychological basis for variations in symptom experiences. Objectives The purposes of this study were to identify and compare symptom clusters in younger (<60 years) and older ($60 years) patients undergoing cancer treatment. Methods. Symptom data from one Australian study and two U.S. studies were combined to conduct this analysis. A total of 593 patients receiving active treatment were dichotomized into younger (<60 years) and older ($60 years) groups. Separate exploratory factor analyses (EFAs) were undertaken within each group to identify symptom clusters from occurrence ratings of the 32 symptoms assessed by the Memorial Symptom Assessment Scale. Results In both groups, a seven-factor solution was selected. Four partially concordant symptom clusters emerged in both groups (i.e., mood/cognitive, malaise, body image, and genitourinary). In the older patients, the three unique clusters reflected physiological changes associated with aging, whereas in the younger group the three unique clusters reflected treatment-related effects. Conclusion The symptom clusters identified in older patients typically included a larger and more diverse range of physical and psychological symptoms. Differences also may be reflective of variations in treatment approaches between age groups. Findings highlight the need for better understanding of variation in treatment and symptom burden between younger and older adults with cancer.

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: A systematic analysis for the Global Burden of Disease Study 2010

BACKGROUND Quantification of the disease burden caused by different risks informs prevention by providing an account of health loss different to that provided by a disease-by-disease analysis. No complete revision of global disease burden caused by risk factors has been done since a comparative risk assessment in 2000, and no previous analysis has assessed changes in burden attributable to risk factors over time. METHODS We estimated deaths and disability-adjusted life years (DALYs; sum of years lived with disability [YLD] and years of life lost [YLL]) attributable to the independent effects of 67 risk factors and clusters of risk factors for 21 regions in 1990 and 2010. We estimated exposure distributions for each year, region, sex, and age group, and relative risks per unit of exposure by systematically reviewing and synthesising published and unpublished data. We used these estimates, together with estimates of cause-specific deaths and DALYs from the Global Burden of Disease Study 2010, to calculate the burden attributable to each risk factor exposure compared with the theoretical-minimum-risk exposure. We incorporated uncertainty in disease burden, relative risks, and exposures into our estimates of attributable burden. FINDINGS In 2010, the three leading risk factors for global disease burden were high blood pressure (7·0% [95% uncertainty interval 6·2-7·7] of global DALYs), tobacco smoking including second-hand smoke (6·3% [5·5-7·0]), and alcohol use (5·5% [5·0-5·9]). In 1990, the leading risks were childhood underweight (7·9% [6·8-9·4]), household air pollution from solid fuels (HAP; 7·0% [5·6-8·3]), and tobacco smoking including second-hand smoke (6·1% [5·4-6·8]). Dietary risk factors and physical inactivity collectively accounted for 10·0% (95% UI 9·2-10·8) of global DALYs in 2010, with the most prominent dietary risks being diets low in fruits and those high in sodium. Several risks that primarily affect childhood communicable diseases, including unimproved water and sanitation and childhood micronutrient deficiencies, fell in rank between 1990 and 2010, with unimproved water and sanitation accounting for 0·9% (0·4-1·6) of global DALYs in 2010. However, in most of sub-Saharan Africa childhood underweight, HAP, and non-exclusive and discontinued breastfeeding were the leading risks in 2010, while HAP was the leading risk in south Asia. The leading risk factor in Eastern Europe, most of Latin America, and southern sub-Saharan Africa in 2010 was alcohol use; in most of Asia, North Africa and Middle East, and central Europe it was high blood pressure. Despite declines, tobacco smoking including second-hand smoke remained the leading risk in high-income north America and western Europe. High body-mass index has increased globally and it is the leading risk in Australasia and southern Latin America, and also ranks high in other high-income regions, North Africa and Middle East, and Oceania. INTERPRETATION Worldwide, the contribution of different risk factors to disease burden has changed substantially, with a shift away from risks for communicable diseases in children towards those for non-communicable diseases in adults. These changes are related to the ageing population, decreased mortality among children younger than 5 years, changes in cause-of-death composition, and changes in risk factor exposures. New evidence has led to changes in the magnitude of key risks including unimproved water and sanitation, vitamin A and zinc deficiencies, and ambient particulate matter pollution. The extent to which the epidemiological shift has occurred and what the leading risks currently are varies greatly across regions. In much of sub-Saharan Africa, the leading risks are still those associated with poverty and those that affect children.

A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.

Preparing engineering graduates for the knowledge economy through blended delivery of mathematics

Contemporary higher education institutions are making significant efforts to develop cohesive, meaningful and effective learning experiences for Science, Technology, Engineering and Mathematics (STEM) curricula to prepare graduates for challenges in the modern knowledge economy, thus enhancing their employability (Carnevale et al, 2011). This can inspire innovative redesign of learning experiences embedded in technology-enhanced educational environments and the development of research-informed, pedagogically reliable strategies fostering interactions between various agents of the learning-teaching process. This paper reports on the results of a project aimed at enhancing students’ learning experiences by redesigning a large, first year mathematics unit for Engineering students at a large metropolitan public university. Within the project, the current study investigates the effectiveness of selected, technology-mediated pedagogical approaches used over three semesters. Grounded in user-centred instructional design, the pedagogical approaches explored the opportunities for learning created by designing an environment containing technological, social and educational affordances. A qualitative analysis of mixed-type questionnaires distributed to students indicated important inter-relations between participants’ frames of references of the learning-teaching process and stressed the importance (and difficulty) of creating appropriate functional context. Conclusions drawn from this study may inform instructional design for blended delivery of STEM-focused programs that endeavor to enhance students’ employability by educating work-ready graduates.

Vascular endothelial growth factor is an autocrine growth factor, signaling through neuropilin-1 in non-small cell lung cancer

Background The VEGF pathway has become an important therapeutic target in lung cancer, where VEGF has long been established as a potent pro-angiogenic growth factor expressed by many types of tumors. While Bevacizumab (Avastin) has proven successful in increasing the objective tumor response rate and in prolonging progression and overall survival in patients with NSCLC, the survival benefit is however relatively short and the majority of patients eventually relapse. The current use of tyrosine kinase inhibitors alone and in combination with chemotherapy has been underwhelming, highlighting an urgent need for new targeted therapies. In this study, we examined the mechanisms of VEGF-mediated survival in NSCLC cells and the role of the Neuropilin receptors in this process. Methods NSCLC cells were screened for expression of VEGF and its receptors. The effects of recombinant VEGF and its blockade on lung tumor cell proliferation and cell cycle were examined. Phosphorylation of Akt and Erk1/2 proteins was examined by high content analysis and confocal microscopy. The effects of silencing VEGF on cell proliferation and survival signaling were also assessed. A Neuropilin-1 stable-transfected cell line was generated. Cell growth characteristics in addition to pAkt and pErk1/2 signaling were studied in response to VEGF and its blockade. Tumor growth studies were carried out in nude mice following subcutaneous injection of NP1 over-expressing cells. Results Inhibition of the VEGF pathway with anti-VEGF and anti-VEGFR-2 antibodies or siRNA to VEGF, NP1 and NP2 resulted in growth inhibition of NP1 positive tumor cell lines associated with down-regulation of PI3K and MAPK kinase signaling. Stable transfection of NP1 negative cells with NP1 induced proliferation in vitro, which was further enhanced by exogenous VEGF. In vivo, NP1 over-expressing cells significantly increased tumor growth in xenografts compared to controls. Conclusions Our data demonstrate that VEGF is an autocrine growth factor in NSCLC signaling, at least in part, through NP1. Targeting this VEGF receptor may offer potential as a novel therapeutic approach and also support the evaluation of the role of NP1 as a biomarker predicting sensitivity or resistance to VEGF and VEGFR-targeted therapies in the clinical arena.

Mood enhancement using smartphone apps

The significant physical, emotional, educational and social developmental challenges faced by adolescents and young adults are associated with high levels of emotional vulnerability. Thus, the development and use of effective emotion-regulation strategies during this period is critical. Music listening is commonly used by young people to identify, express, enhance and regulate their emotions. Modern mobile technology provides an engaging, easily accessible means of assisting young people with identifying and managing emotions through music. A systematic contextual review of iPhone applications addressing emotions through music was conducted. Their quality was evaluated by two independent raters using the Mobile App Rating Scale (MARS). Three participatory design workshops (PDW; N=13, 6 males, 7 females; age 15-25) were conducted, exploring young people’s use of music to enhance wellbeing. Young people were also asked to trial existing mood and music apps and to conceptualise their ultimate mood-targeting music application. Of the identified 117 music apps, 20 met inclusion criteria (to play songs, not sounds; priced below $5.00). Characteristics and overall quality of the music apps are described and key features of the five highest- rating apps are presented. Thematic analysis of the PDW content identified the following music affect- regulation strategies: relationship building, modifying cognitions, modifying emotions, and immersing in emotions (i.e. habituation or mood enhancement). The application of key learnings from the mobile app review and PDW to the design and development of the new music eScape app will be presented. Implications for future research and for applying the new app in clinical practice are discussed.

Positioning as a source of competitive advantage: Benchmarking Rotorua’s position as a domestic short break holiday destination

Travellers are spoilt by holiday choice, and yet will usually only seriously consider a few destinations during the decision process. With thousands of destination marketing organisations (DMOs) competing for attention, places are becoming increasingly substitutable. The study of destination competitiveness is an emerging field, and thesis contributes to an enhanced understanding by addressing three topics that have received relatively little attention in the tourism literature: destination positioning, the context of short break holidays, and domestic travel in New Zealand. A descriptive model of positioning as a source of competitive advantage is developed, and tested through 12 propositions. The destination of interest is Rotorua, which was arguably New Zealand’s first tourist destination. The market of interest is Auckland, which is Rotorua’s largest visitor market. Rotorua’s history is explored to identify factors that may have contributed to the destination’s current image in the Auckland market. A mix of qualitative and quantitative procedures is then utilised to determine Rotorua’s position, relative to a competing set of destinations. Based on an applied research problem, the thesis attempts to bridge the gap between academia and industry by providing useable results and benchmarks for five regional tourism organisations (RTOs). It is proposed that, in New Zealand, the domestic short break market represents a valuable opportunity not explicitly targeted by the competitive set of destinations. Conceptually, the thesis demonstrates the importance of analysing a destination’s competitive position, from the demand perspective, in a travel context; and then the value of comparing this ‘ideal’ position with that projected by the RTO. The thesis concludes Rotorua’s market position in the Auckland short break segment represents a source of comparative advantage, but is not congruent with the current promotional theme, which is being used in all markets. The findings also have implications for destinations beyond the context of the thesis. In particular, a new definition for ‘destination attractiveness’ is proposed, which warrants consideration in the design of future destination positioning analyses.

Risk factors for hospital re-presentation among older adults following fragility fractures: Protocol for a systematic review

Background After being discharged from hospital following the acute management of a fragility fracture, older adults may re-present to hospital emergency departments in the post-discharge period. Early re-presentation to hospital, which includes hospital readmissions, and emergency department presentations without admission, may be considered undesirable for individuals, hospital institutions and society. The identification of modifiable risk factors for hospital re-representation following initial fracture management may prove useful for informing policy or practice initiatives that seek to minimise the need for older adults to re-present to hospital early after they have been discharged from their initial inpatient care. The purpose of this systematic review is to identify correlates of hospital re-presentation in older patients who have been discharged from hospital following clinical management of fragility fractures. Methods/Design The review will follow the PRISMA-P reporting guidelines for systematic reviews. Four electronic databases (Pubmed, CINAHL, Embase, and Scopus) will be searched. A suite of search terms will identify peer-reviewed articles that have examined the correlates of hospital re-presentation in older adults (mean age of 65 years or older) who have been discharged from hospital following treatment for fragility fractures. The Effective Public Health Practice Project Quality Assessment Tool for Quantitative Studies will be used to assess the quality of the studies. The strength of evidence will be assessed through best evidence synthesis. Clinical and methodological heterogeneity across studies are likely to impede meta-analyses. Discussion The best evidence synthesis will outline correlates of hospital re-presentations in this clinical group. This synthesis will take into account potential risks of bias for each study, while permitting inclusion of findings from a range of quantitative study designs. It is anticipated that findings from the review will be useful in identifying potentially modifiable risk factors that have relevance in policy, practice and research priorities to improve the management of patients with fragility fractures. Systematic Review Registration PROSPERO CRD42015019379

Destination Marketing Essentials [2nd Edition]

Destination Marketing offers the reader an integrated and comprehensive overview of the key challenges and constraints facing DMOs and how destination marketing can be planned, implemented and evaluated to achieve successful destination competitiveness. This new 2nd Edition has been revised and updated to include: • new slim - lined 15 chapter structure • new chapters on Destination Competitiveness and Technology • new and updated case studies throughout including emerging markets • new content on social media marketing in destination marketing organisations and sustainable destination marketing • additional online resources for lecturers and students including PPT’s, test bank and video links. It is written in an engaging style and applies theory to a range of tourism destinations at the consumer, business, national and international level by using topical examples.

Destination brand performance measurement over time: Tracking consumer perceptions of a competitive set of destinations over a 10 year period

There has been a paucity of research published in relation to the temporal aspect of destination image change over time. Given increasing investments in destination branding, research is needed to enhance understanding of how to monitor destination brand performance, of which destination image is the core construct, over time. This article reports the results of four studies tracking brand performance of a competitive set of five destinations, between 2003 and 2012. Results indicate minimal changes in perceptions held of the five destinations of interest over the 10 years, supporting the assertion of Gartner (1986) and Gartner and Hunt (1987) that destination image change will only occur slowly over time. While undertaken in Australia, the research approach provides DMOs in other parts of the world with a practical tool for evaluating brand performance over time; in terms of measures of effectiveness of past marketing communications, and indicators of future performance.

Adolescent self-reported physical activity and autonomy: A case for constrained and structured environments?

The provision of autonomy supportive environments that promote physical activity engagement have become popular in contemporary youth settings. However, questions remain about whether adolescent perceptions of their autonomy have implications for physical activity. The purpose of this investigation was to examine the association between adolescents’ self-reported physical activity and their perceived autonomy. Participants (n = 384 adolescents) aged between 12 and 15 years were recruited from six secondary schools in metropolitan Brisbane, Australia. Self-reported measures of physical activity and autonomy were obtained. Logistic regression with inverse probability weights were used to examine the association between autonomy and the odds of meeting youth physical activity guidelines. Autonomy (OR 0.61, 95% CI 0.49-0.76) and gender (OR 0.62, 95% CI 0.46-0.83) were negatively associated with meeting physical activity guidelines. However, the model explained only a small amount of the variation in whether youth in this sample met physical activity guidelines (R2 = 0.023). For every 1 unit decrease in autonomy (on an index from 1 to 5), participants were 1.64 times more likely to meet physical activity guidelines. The findings, which are at odds with several previous studies, suggest that interventions designed to facilitate youth physical activity should limit opportunities for youth to make independent decisions about their engagement. However, the small amount of variation explained by the predictors in the model is a caveat, and should be considered prior to applying such suggestions in practical settings. Future research should continue to examine a larger age range, longitudinal observational or intervention studies to examine assertions of causality, as well as objective measurement of physical activity.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.