Human breast tumor slices as an alternative approach to cell lines to individualize research for each patient

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Writing together, learning together : the value and effectiveness of a research writing group for doctoral students

The high level of scholarly writing required for a doctoral thesis is a challenge for many research students. However, formal academic writing training is not a core component of many doctoral programs. Informal writing groups for doctoral students may be one method of contributing to the improvement of scholarly writing. In this paper, we report on a writing group that was initiated by an experienced writer and higher degree research supervisor to support and improve her doctoral students’ writing capabilities. Over time, this group developed a workable model to suit their varying needs and circumstances. The model comprised group sessions, an email group, and individual writing. Here, we use a narrative approach to explore the effectiveness and value of our research writing group model in improving scholarly writing. The data consisted of doctoral students’ reflections to stimulus questions about their writing progress and experiences. The stimulus questions sought to probe individual concerns about their own writing, what they had learned in the research writing group, the benefits of the group, and the disadvantages and challenges to participation. These reflections were analysed using thematic analysis. Following this analysis, the supervisor provided her perspective on the key themes that emerged. Results revealed that, through the writing group, members learned technical elements (e.g., paragraph structure), non-technical elements (e.g., working within limited timeframes), conceptual elements (e.g., constructing a cohesive arguments), collaborative writing processes, and how to edit and respond to feedback. In addition to improved writing quality, other benefits were opportunities for shared writing experiences, peer support, and increased confidence and motivation. The writing group provides a unique social learning environment with opportunities for: professional dialogue about writing, peer learning and review, and developing a supportive peer network. Thus our research writing group has proved an effective avenue for building doctoral students’ capability in scholarly writing. The proposed model for a research writing group could be applicable to any context, regardless of the type and location of the university, university faculty, doctoral program structure, or number of postgraduate students. It could also be used within a group of students with diverse research abilities, needs, topics and methodologies. However, it requires a group facilitator with sufficient expertise in scholarly writing and experience in doctoral supervision who can both engage the group in planned writing activities and also capitalise on fruitful lines of discussion related to students’ concerns as they arise. The research writing group is not intended to replace traditional supervision processes nor existing training. However it has clear benefits for improving scholarly writing in doctoral research programs particularly in an era of rapidly increasing student load.

Exponential asymptotics with multiple stokes lines

When asymptotic series methods are applied in order to solve problems that arise in applied mathematics in the limit that some parameter becomes small, they are unable to demonstrate behaviour that occurs on a scale that is exponentially small compared to the algebraic terms of the asymptotic series. There are many examples of physical systems where behaviour on this scale has important effects and, as such, a range of techniques known as exponential asymptotic techniques were developed that may be used to examinine behaviour on this exponentially small scale. Many problems in applied mathematics may be represented by behaviour within the complex plane, which may subsequently be examined using asymptotic methods. These problems frequently demonstrate behaviour known as Stokes phenomenon, which involves the rapid switches of behaviour on an exponentially small scale in the neighbourhood of some curve known as a Stokes line. Exponential asymptotic techniques have been applied in order to obtain an expression for this exponentially small switching behaviour in the solutions to orginary and partial differential equations. The problem of potential flow over a submerged obstacle has been previously considered in this manner by Chapman & Vanden-Broeck (2006). By representing the problem in the complex plane and applying an exponential asymptotic technique, they were able to detect the switching, and subsequent behaviour, of exponentially small waves on the free surface of the flow in the limit of small Froude number, specifically considering the case of flow over a step with one Stokes line present in the complex plane. We consider an extension of this work to flow configurations with multiple Stokes lines, such as flow over an inclined step, or flow over a bump or trench. The resultant expressions are analysed, and demonstrate interesting implications, such as the presence of exponentially sub-subdominant intermediate waves and the possibility of trapped surface waves for flow over a bump or trench. We then consider the effect of multiple Stokes lines in higher order equations, particu- larly investigating the behaviour of higher-order Stokes lines in the solutions to partial differential equations. These higher-order Stokes lines switch off the ordinary Stokes lines themselves, adding a layer of complexity to the overall Stokes structure of the solution. Specifically, we consider the different approaches taken by Howls et al. (2004) and Chap- man & Mortimer (2005) in applying exponential asymptotic techniques to determine the higher-order Stokes phenomenon behaviour in the solution to a particular partial differ- ential equation.

Comparative communication research : Australian and New Zealand communication research in an international context

This paper raises the question of whether comparative national models of communications research can be developed, along the lines of Hallin and Mancini’s (2004) analysis of comparative media policy, or the work of Perraton and Clift (2004) on comparative national capitalisms. Taking consideration of communications research in Australia and New Zealand as its starting point, the paper will consider what are relevant variables in shaping an “intellectual milieu” for communications research in these countries, as compared to those of Europe, North America and Asia. Some possibly relevant variables include: • Type of media system (e.g. how significant is public service media?); • Political culture (e.g. are there significant left-of-centre political parties?); • Dominant intellectual traditions; • Level and types of research funding; • Overall structure of higher education system, and where communications sits within it. In considering whether such an exercise can or should be undertaken, we can also evaluate, as Hallin and Mancini do, the significance of potentially homogenizing forces. These would include globalization, new media technologies, and the rise of a global “audit culture”. The paper will raise these issues as questions that emerge as we consider, as Curran and Park (2000) and Thussu (2009) have proposed, what a “de-Westernized” media and communications research paradigm may look like.

Aligning communication, cultural and media studies research and scholarship with industry and policy : Australian instances

This article reflects on aspects of what is claimed to be the distinctiveness of Australian communication, cultural and media studies, focusing on two cases – the cultural policy debate in the 1990s, and the concept of creative industries in the 2000s – and the relations between them, which highlight the alignment of research and scholarship with industry and policy and with which the author has been directly involved. Both ‘moments’ have been controversial; the three main lines of critique of such alignment of research and scholarship with industry and policy (its untoward proximity to tenets of the dominant neo-liberal ideology; the evacuation of cultural value by the economic; and the possible loss of critical vocation of the humanities scholar) are debated.

CDKN2A/p16 is inactivated in most melanoma cell lines

The CDKN2A gene maps to chromosome 9p21-22 and is responsible for melanoma susceptibility in some families. Its product, p16, binds specifically to CDK4 and CDK6 in vitro and in vivo, inhibiting their kinase activity. CDKN2A is homozygously deleted or mutated in a large proportion of tumor cell lines and some primary tumors, including melanomas. The aim of this study was to investigate the involvement of CDKN2A and elucidate the mechanisms of p16 inactivation in a panel of 60 cell lines derived from sporadic melanomas. Twenty-six (43%) of the melanoma lines were homozygously deleted for CDKN2A, and an additional 15 (25%) lines carried missense, nonsense, or frameshift mutations. All but one of the latter group were shown by microsatellite analysis to be hemizygous for the region of 9p surrounding CDKN2A. p16 was detected by Western blotting in only five of the cell lines carrying mutations. Immunoprecipitation of p16 in these lines, followed by Western blotting to detect the coprecipitation of CDK4 and CDK6, revealed that p16 was functionally compromised in all cell lines but the one that carried a heterozygous CDKN2A mutation. In the remaining 19 lines that carried wild-type CDKN2A alleles, Western blot analysis and immunoprecipitation indicated that 11 cell lines expressed a wild-type protein. Northern blotting was performed on the remaining eight cell lines and revealed that one cell line carried an aberrantly sized RNA transcript, and two other cell lines failed to express RNA. The promoter was found to be methylated in five cell lines that expressed CDKN2A transcript but not p16. Presumably, the message seen by Northern blotting in these cell lines is the result of cross-hybridization of the total cDNA probe with the exon 1beta transcript. Microsatellite analysis revealed that the majority of these cell lines were hemi/homozygous for the region surrounding CDKN2A, indicating that the wild-type allele had been lost. In the 11 cell lines that expressed functional p16, microsatellite analysis revealed loss of heterozygosity at the markers immediately surrounding CDKN2A in five cases, and the previously characterized R24C mutation of CDK4 was identified in one of the remaining 6 lines. These data indicate that 55 of 60 (92%) melanoma cell lines demonstrated some aberration of CDKN2A or CDK4, thus suggesting that this pathway is a primary genetic target in melanoma development.

Mutations in exon 3 of the beta-catenin gene are rare in melanoma cell lines

Mutations in exon 3 of the CTNNB1 gene encoding beta-catenin have been reported in colorectal cancer cell lines and tumours. Although one study reported mutations or deletions affecting beta-catenin in 20% of melanoma cell lines, subsequent reports detected a much lower frequency of aberrations in uncultured melanomas. To determine whether this difference in mutation frequency reflected an in vitro culturing artefact, exon 3 of CTNNB1 was screened in a panel of 62 melanoma cell lines. In addition, reverse transcription-polymerase chain reaction (RT-PCR) was performed to detect intragenic deletions affecting exon 3. One out of 62 (1.6%) cell lines was found to carry a mutation, indicating that aberration of the Wnt-1/wingless pathway through activation of beta-catenin is a rare event, even in melanoma cell lines.

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.

Genetic diversity in three redclaw crayfish (Cherax quadricarinatus, von Martens) lines developed in culture in China

The redclaw crayfish Cherax quadricarinatus (von Martens) accounts for the entire commercial production of freshwater crayfish in Australia. Two forms have been recognized, an 'Eastern' form in northern Queensland and a 'Western' form in the Northern Territory and far northern Western Australia. To date, only the Eastern form has been exported overseas for culture (including to China). The genetic structure of three Chinese redclaw crayfish culture lines from three different geographical locations in China (Xiamen in Fujian Province, Guangzhou in Guangdong Province and Chongming in Shanghai) were investigated for their levels and patterns of genetic diversity using microsatellite markers. Twenty-eight SSR markers were isolated and used to analyse genetic diversity levels in three redclaw crayfish culture lines in China. This study set out to improve the current understanding of the molecular genetic characteristics of imported strains of redclaw crayfish reared in China. Microsatellite analysis revealed moderate allelic and high gene diversity in all three culture lines. Polymorphism information content estimates for polymorphic loci varied between 0.1168 and 0.8040, while pairwise F ST values among culture lines were moderate (0.0020-0.1244). The highest estimate of divergence was evident between the Xiamen and Guangzhou populations.

White Lines: The Intercultural Politics of Everyday Movement in Local Spaces

This article draws on research into racist vilification experienced by young Arab and Muslim Australians especially since 11 September 2001, to explore the links between public space, movement and national belonging, and the spatial regulation of cultural difference that functions in Australia. The authors analyse the way that the capacity to experience forms of national belonging and cultural citizenship is shaped by inclusion within or exclusion from local as well as nationally significant public spaces. While access to public space and freedom to move are conventionally seen as fundamental to a democratic state, these are often seen in abstract terms. This article emphasises how movement in public space is a very concrete dimension of our experience of freedom, in showing how incivilities directed against Arab and Muslim Australians have operated pedagogically as a spatialised regulation of national belonging. The article concludes by examining how processes associated with the Cronulla riots of December 2005 have retarded the capacities of Muslim and Arab Australians to negotiate within and across spaces, diminishing their opportunities to invest in local and national spaces, shrinking their resources and opportunities for place-making in public space.

Passenger transmission and productiveness of transit lines with high loads

Deterministic transit capacity analysis applies to planning, design and operational management of urban transit systems. The Transit Capacity and Quality of Service Manual (1) and Vuchic (2, 3) enable transit performance to be quantified and assessed using transit capacity and productive capacity. This paper further defines important productive performance measures of an individual transit service and transit line. Transit work (p-km) captures the transit task performed over distance. Passenger transmission (p-km/h) captures the passenger task delivered by service at speed. Transit productiveness (p-km/h) captures transit work performed over time. These measures are useful to operators in understanding their services’ or systems’ capabilities and passenger quality of service. This paper accounts for variability in utilized demand by passengers along a line and high passenger load conditions where passenger pass-up delay occurs. A hypothetical case study of an individual bus service’s operation demonstrates the usefulness of passenger transmission in comparing existing and growth scenarios. A hypothetical case study of a bus line’s operation during a peak hour window demonstrates the theory’s usefulness in examining the contribution of individual services to line productive performance. Scenarios may be assessed using this theory to benchmark or compare lines and segments, conditions, or consider improvements.