Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis

Cell line array (CMA) and tissue microarray (TMA) technologies are high-throughput methods for analysing both the abundance and distribution of gene expression in a panel of cell lines or multiple tissue specimens in an efficient and cost-effective manner. The process is based on Kononen's method of extracting a cylindrical core of paraffin-embedded donor tissue and inserting it into a recipient paraffin block. Donor tissue from surgically resected paraffin-embedded tissue blocks, frozen needle biopsies or cell line pellets can all be arrayed in the recipient block. The representative area of interest is identified and circled on a haematoxylin and eosin (H&E)-stained section of the donor block. Using a predesigned map showing a precise spacing pattern, a high density array of up to 1,000 cores of cell pellets and/or donor tissue can be embedded into the recipient block using a tissue arrayer from Beecher Instruments. Depending on the depth of the cell line/tissue removed from the donor block 100-300 consecutive sections can be cut from each CMA/TMA block. Sections can be stained for in situ detection of protein, DNA or RNA targets using immunohistochemistry (IHC), fluorescent in situ hybridisation (FISH) or mRNA in situ hybridisation (RNA-ISH), respectively. This chapter provides detailed methods for CMA/TMA design, construction and analysis with in-depth notes on all technical aspects including tips to deal with common pitfalls the user may encounter. © Springer Science+Business Media, LLC 2011.

From words to integers and beyond in corporate life

Poets have a licence to couch great truths in succinct, emotionally powerful, and perhaps slightly mysterious and ambiguous ways. On the other hand, it is the task of academics to explore such truths intellectually, in depth and detail, identifying the key constructs and their underlying relations and structures, hopefully without impairing the essential truth. So it could be said that in January 2013, around 60 academics gathered at the University of Texas, Austin under the benign and encouraging eye of their own muse, Professor Rod Hart, to play their role in exploring and explaining the underlying truth of Yan Zhen’s words. The goals of this chapter are quite broad. Rod was explicit and yet also somewhat Delphic in his expectations and aspirations for the chapter. Even though DICTION was a key analytic tool in most chapters, this chapter was not to be about DICTION per se, or simply a critique of the individual chapters forming this section of the book. Rather DICTION and these studies, as well as some others that got our attention, were to be more a launching pad for observations on what they revealed about the current state of understanding and research into the language of institutions, as well as some ‘adventurous’, but not too outlandish reflections on future challenges and opportunities.

A Bayesian regression approach to assess uncertainty in pollutant wash-off modelling

Due to knowledge gaps in relation to urban stormwater quality processes, an in-depth understanding of model uncertainty can enhance decision making. Uncertainty in stormwater quality models can originate from a range of sources such as the complexity of urban rainfall-runoff-stormwater pollutant processes and the paucity of observed data. Unfortunately, studies relating to epistemic uncertainty, which arises from the simplification of reality are limited and often deemed mostly unquantifiable. This paper presents a statistical modelling framework for ascertaining epistemic uncertainty associated with pollutant wash-off under a regression modelling paradigm using Ordinary Least Squares Regression (OLSR) and Weighted Least Squares Regression (WLSR) methods with a Bayesian/Gibbs sampling statistical approach. The study results confirmed that WLSR assuming probability distributed data provides more realistic uncertainty estimates of the observed and predicted wash-off values compared to OLSR modelling. It was also noted that the Bayesian/Gibbs sampling approach is superior compared to the most commonly adopted classical statistical and deterministic approaches commonly used in water quality modelling. The study outcomes confirmed that the predication error associated with wash-off replication is relatively higher due to limited data availability. The uncertainty analysis also highlighted the variability of the wash-off modelling coefficient k as a function of complex physical processes, which is primarily influenced by surface characteristics and rainfall intensity.

Exploring pedestrian accessibility and walkability : insight from public place observations in inner-urban higher density Brisbane, Australia

As planners work to create more sustainable and liveable urban environments, a priority is to transition away from prioritising the automobile and towards enhancing the pedestrian experience. Thus, this research explores the experience of pedestrian accessibility in inner-urban higher-density Brisbane in Australia, drawing on findings from semi-structured in-depth interviews with 24 residents and over 100 hours of public place observations in three case-study neighbourhoods. The interviews took place in residents homes and explored their experience of higher density living and their neighbourhood, whilst observations were recorded through a combination of methods including photographs, sketch maps, recordings and field journals. Observation locations included retail and commercial space, roads, parkland and open space, with multiple observations at each location. A thematic analysis identified common themes in both interviews and the observations, with this paper focusing on residents’ lived experience in urban built environments. This analysis revealed that pedestrian accessibility is linked to access to local amenities and direct routes, aesthetics, sense of community, ownership of space and safety. In particular, observations revealed how pedestrian accessibility and route-taking works with, against or in spite of the design features of urban environments, as well as the importance of the social use of the built environment. Residents spoke about although walking quick and preferred for local amenities, the decision to walk was moderated by factors such as time of day and perceived safety. Measures to ensure and improve the pedestrian accessibility of urban areas needs to take into account the propensity for people to prefer and improvise direct routes (often to the detriment of traffic safety considerations), the importance of ongoing maintenance and upgrading of walking infrastructure and the importance of aesthetically pleasing and safe walking environments. By combining interviews and observations, this research highlights the current dominance of the automobile culture in Brisbane and the layers of meaning, experiences and complexity hidden within the pedestrian experience.

Dimensions of Indigenous journalism culture : exploring Maori news-making in Aotearoa New Zealand

Indigenous news media have experienced significant growth across the globe in recent years, but they have received only limited attention in mainstream society or the journalism and communication research community. Yet, Indigenous journalism is playing an arguably increasingly important role in contributing to Indigenous politics and identities, and is worthy of closer analysis. Using in-depth interviews, this article provides an overview of the main dimensions of Indigenous journalism as they can be found in the journalism culture of Māori journalists in Aotearoa New Zealand. It argues that Māori journalists see their role as providing a counter-narrative to mainstream media reporting and as contributing to Indigenous empowerment and revitalization of their language. At the same time, they view themselves as watchdogs, albeit within a culturally specific framework that has its own constraints. The article argues that the identified dimensions are reflective of evidence on Indigenous journalism from across the globe.

Cultural forces in journalism : the impact of cultural values on Māori journalists’ professional views

Social system-level analyses of journalism have tended to focus on political and economic influences, at the expense of other factors, such as the role that culture and cultural values play in shaping journalists' professional views and practices. This paper identifies cultural values as a particularly fruitful area for providing a more nuanced analysis of journalism culture. It examines this issue in the context of in-depth interviews with 20 M?ori journalists from Aotearoa New Zealand. The study finds that Indigenous journalism in that country is strongly influenced by M?ori cultural values, such as showing respect to others, following cultural protocols, and making use of culturally-specific language. Cultural limitations are also identified in the form of the social structures of M?ori society, and journalists' strategies in working around these are discussed. The paper highlights the implications a renewed focus on cultural values can have for the study of journalism culture more broadly.

Mediating orientation and self-expression in the world of consumption : Australian and German lifestyle journalists' professional views

Despite having experienced rapid popularity over the past two decades, lifestyle journalism is still somewhat neglected by academic researchers. So far mostly explored as either part of wider lifestyle programming, particularly on television, or in terms of individual sub-fields, such as travel, fashion or food journalism, lifestyle journalism is in need of scholarly analysis particularly in the area of production, based on the increasing importance which the field has in influencing audiences’ ways of life. This study explores the professional views of 89 Australian and German lifestyle journalists through in-depth interviews in order to explore the ways in which they engage in processes of influencing audiences’ self-expression, identities and consumption behaviors. The article argues that through its work, lifestyle journalism is a significant shaper of identities in today’s consumer societies.

Exploring emotions on #auspol : polarity, conservativism and public performance in the Twitter debate on Australian politics

The affective communication patterns of conversations on Twitter can provide insights into the culture of online communities. In this paper we apply a combined quantitative and qualitative approach to investigate the structural make-up and emotional content of tweeting activity around the hashtag #auspol (for Australian politics) in order to highlight the polarity and conservativism that characterise this highly active community of politically engaged individuals. We document the centralised structure of this particular community, which is based around a deeply committed core of contributors. Through in-depth content analysis of the tweets of participants to the online debate we explore the communicative tone, patterns of engagement and thematic drivers that shape the affective character of the community and their effect on its cohesiveness. In this way we provide a comprehensive account of the complex techno-social, linguistic and cultural factors involved in conversations that are shaped in the Twittersphere.

Doing cultural work : local postcard production and place identity in a rural shire

Studies of place construction in the rural studies literature have largely privileged the role of professionals over that of local lay actors. This paper contributes to redressing this imbalance through a critical case-study of lay postcard production in a rural shire. Drawing on original, qualitative research conducted in the Shire of Ravensthorpe, Western Australia, including in-depth interviews with key participants, the analysis focuses on this lay production—undertaken in the main by women—as cultural work. By emphasising the work of making the postcards along with the cultural work these postcards achieve, this examination foregrounds intersections of material and imagined ruralities. In the process, this study highlights the complexity and importance of this lay contribution to place identity, particularly as positioned within what may be considered rural cultural work.

Same but different? Mobile technology adoption in China

Purpose This paper seeks to answer two research questions which are “What are key factors which influence Chinese to adopt mobile technology?” and “Do these key factors differ from factors which are identified from Western context?” Design/methodology The findings from a pilot study with 45 in-depth interviews are used to develop questionnaires and test across 800 residents from the three research cities. The data were analyzed by Structural Equation Modelling together with Multi-group Analysis. Findings Our data suggest eight important concepts, i.e. utilitarian expectation, hedonic expectation, status gains, status loss avoidance, normative influence, external influence, cost, and quality concern, are influential factors affecting users’ intentions to adopt 3G mobile technology. Differences are found between the samples in the three research cities in the effect of hedonic expectation, status gains, status loss avoidance, and normative influence on mobile technology adoption intention. Research limitations/implications: As the stability of intentions may change over time, only measuring intentions might be inadequate in predicting actual adoption behaviors. However, the focus on potential users is thought to be appropriate, given that the development of 3G is still in its infancy in China. Originality/value Previous research into Information Technology (IT) adoption among Chinese users has not paid attention to regional diversity. Some research considered China as a large single market and some was conducted in only one province or one city. Culturally, China is a heterogeneous country.

Confirmatory factor analysis of the baby eating behaviour questionnaire and associations with infant weight, gender and feeding mode in an Australian sample

The aim of this study was to evaluate the factor structure of the Baby Eating Behaviour Questionnaire (BEBQ) in an Australian community sample of mother-infant dyads. A secondary aim was to explore the relationship between the BEBQ subscales and infant gender, weight and current feeding mode. Confirmatory factor analysis (CFA) utilising structural equation modelling examined the hypothesised 4-factor model of the BEBQ. Only mothers (N=467) who completed all items on the BEBQ (infant age: M=17 weeks, SD=3 weeks) were included in the analysis. The original 4-factor model did not provide an acceptable fit to the data due to poor performance of the Satiety responsiveness factor. Removal of this factor (3 items) resulted in a well-fitting 3-factor model. Cronbach’s α was acceptable for the Enjoyment of food (α=0.73), Food responsiveness (α=0.78) and Slowness in eating (α=0.68) subscales but low for the Satiety responsiveness (α=0.56) subscale. Enjoyment of food was associated with higher infant weight whereas Slowness in eating and Satiety responsiveness were both associated with lower infant weight. Differences on all four subscales as a function of feeding mode were observed. This study is the first to use CFA to evaluate the hypothesised factor structure of the BEBQ. Findings support further development work on the Satiety responsiveness subscale in particular, but confirm the utility of the Enjoyment of food, Food responsiveness and Slowness in eating subscales.

Use your freedom of choice : reasons for choosing homeschool in Australia

In Australia, the decision to home educate is becoming increasingly popular (cf. Harding & Farrell, 2003; Townsend, 2012). In spite of its increasing popularity, the reasons home education is chosen by Australian families is under-researched (cf. Jackson & Allan, 2010). This paper reports on a case study that set out to explore the links between families that unschool and the parenting philosophies they follow. In- depth, qualitative interviews were conducted with a group of home education families in one of Australia’s most populated cities. Data were analysed using Critical Discourse Analysis. The analysis revealed that there were links between the parents’ beliefs about home education and their adherence to Attachment Parenting.

Differential subcellular and extracellular localisations of proteins required for insulin-like growth factor- and extracellular matrix-induced signalling events in breast cancer progression

Background: Cancer metastasis is the main contributor to breast cancer fatalities as women with the metastatic disease have poorer survival outcomes than women with localised breast cancers. There is an urgent need to develop appropriate prognostic methods to stratify patients based on the propensities of their cancers to metastasise. The insulin-like growth factor (IGF)-I:IGF binding protein (IGFBP):vitronectin complexes have been shown to stimulate changes in gene expression favouring increased breast cancer cell survival and a migratory phenotype. We therefore investigated the prognostic potential of these IGF- and extracellular matrix (ECM) interaction-induced proteins in the early identification of breast cancers with a propensity to metastasise using patient-derived tissue microarrays. Methods: Semiquantitative immunohistochemistry analyses were performed to compare the extracellular and subcellular distribution of IGF- and ECM-induced signalling proteins among matched normal, primary cancer and metastatic cancer formalin-fixed paraffin-embedded breast tissue samples. Results: The IGF- and ECM-induced signalling proteins were differentially expressed between subcellular and extracellular localisations. Vitronectin and IGFBP-5 immunoreactivity was lower while β1 integrin immunoreactivity was higher in the stroma surrounding metastatic cancer tissues, as compared to normal breast and primary cancer stromal tissues. Similarly, immunoreactive stratifin was found to be increased in the stroma of primary as well as metastatic breast tissues. Immunoreactive fibronectin and β1 integrin was found to be highly expressed at the leading edge of tumours. Based on the immunoreactivity it was apparent that the cell signalling proteins AKT1 and ERK1/2 shuffled from the nucleus to the cytoplasm with tumour progression. Conclusion: This is the first in-depth, compartmentalised analysis of the distribution of IGF- and ECM-induced signalling proteins in metastatic breast cancers. This study has provided insights into the changing pattern of cellular localisation and expression of IGF- and ECM-induced signalling proteins in different stages of breast cancer. The differential distribution of these biomarkers could provide important prognostic and predictive indicators that may assist the clinical management of breast disease, namely in the early identification of cancers with a propensity to metastasise, and/or recur following adjuvant therapy.

Productivity analysis with CO2 emissions in Japan

This article measures Japanese prefectures' productivity from 1991 to 2002, taking CO2 emissions into consideration, and examines the factors that impact on productivity. We use the data envelopment analysis and measure the Luenberger productivity indicator, incorporating CO2 emissions in the analysis. Our results show that productivity was decreasing during the period of investigation. According to the results of the generalized method of moment estimation, the operations rate, the share of the energy intensive industries and social capital significantly impact on productivity.

Evaluation of assessment in the context of work-based learning: Qualitative perspectives of new graduates

Aim Evaluation or assessment of competence is an important step to ensure the safety and efficacy of health professionals, including dietitians. Most competency-based assessment studies are focussed on valid and reliable methods of assessment for the preparation of entry-level dietitians, few papers have explored student dietitians’ perceptions of these evaluations. This study aimed to explore the perceptions of recent graduates from accredited nutrition and dietetics training programs in Australia. It also aimed to establish the relevance of competency-based assessment to adequately prepare them for entry-level work roles. Methods A purposive sample of newly-graduated dietitians with a range of assessment experiences and varied employment areas was recruited. A qualitative approach, using in-depth interviews with 13 graduates, with differing assessment experiences was undertaken. Graduates were asked to reflect upon their competency-based assessment experiences whilst a student. Data was thematically analysed by multiple authors. Results Four themes emerged from the data analysis: (i) Transparency and consistency are critical elements of work-based competency assessment. (ii) Students are willing to take greater responsibility in their assessment process. (iii) Work-based competency assessment prepares students for employment. (iv) The relationship between students and their assessors can impact on the student experience and their assessment performance. Conclusions Understanding this unique perspective of students can improve evaluation of future health professionals and assist in designing valid competency-based assessment approaches.