Multiplexed tandem polymerase chain reaction identifies strong expression of oestrogen receptor and Her-2 from single, formalin-fixed, paraffin-embedded breast cancer sections

Aim To establish the suitability of multiplex tandem polymerase chain reaction (MT-PCR) for rapid identification of oestrogen receptor (ER) and Her-2 status using a single, formalin-fixed, paraffin-embedded (FFPE) breast tumour section. Methods Tissue sections from 29 breast tumours were analysed by immunohistochemistry (IHC) and fluorescence in situ hybridisation (FISH). RNA extracted from 10μm FFPE breast tumour sections from 24 of 29 tumours (14 ER positive and 5 Her-2 positive) was analysed by MT-PCR. After establishing a correlation between IHC and/or FISH and MT-PCR results, the ER/Her-2 status of a further 32 randomly selected, archival breast tumour specimens was established by MT-PCR in a blinded fashion, and compared to IHC/FISH results. Results MT-PCR levels of ER and Her-2 showed good concordance with IHC and FISH results. Furthermore, among the ER positive tumours, MT-PCR provided a quantitative score with a high dynamic range. Threshold values obtained from this data set applied to 32 archival tumour specimens showed that tumours strongly positive for ER and/or Her-2 expression were easily identified by MT-PCR. Conclusion MT-PCR can provide rapid, sensitive and cost-effective analysis of FFPE material and may prove useful as triage to identify patients suited to endocrine or trastuzumab (Herceptin) treatment.

A natural oil-based emulsion containing allantoin versus aqueous cream for managing radiation-induced skin reactions in patients with cancer : a phase III double-blind randomised controlled trial

Purpose To investigate the effects of a natural oil-based emulsion containing allantoin versus aqueous cream for preventing and managing radiation induced skin reactions (RISR). Methods and Materials A total of 174 patients were randomised and participated in the study. Patients either received Cream 1 (the natural oil-based emulsion containing allantoin) or Cream 2 (aqueous cream). Skin toxicity, pain, itching and skin-related quality of life scores were collected for up to four weeks after radiation treatment. Results Patients who received Cream 1 had a significantly lower average level of Common Toxicity Criteria at week 3 (p<0.05), but had statistically higher average levels of skin toxicity at weeks 7, 8 and 9 (all p<0.001). Similar results were observed when skin toxicity was analysed by grades. With regards to pain, patients in the Cream 2 group had a significantly higher average level of worst pain (p<0.05) and itching (p=0.046) compared to the Cream 1 group at week 3, however these differences were not observed at other weeks. In addition, there was a strong trend for Cream 2 to reduce the incidence of grade 2 or more skin toxicity in comparison to Cream 1 (p=0.056). Overall, more participants in the Cream 1 group were required to use another topical treatment at weeks 8 (p=0.049) and 9 (p=0.01). Conclusion The natural oil-based emulsion containing allantoin appears to have similar effects for managing skin toxicity compared to aqueous cream up to week 5, however, it becomes significantly less effective at later weeks into the radiation treatment and beyond treatment completion (week 6 and beyond). There were no major differences in pain, itching and skin-related quality of life. In light of these results, clinicians and patients can base their decision on costs and preferences. Overall, aqueous cream appears to be a more preferred option.

Accurately defining the reference condition for summary biotic metrics: A comparison of four approaches

Protocols for bioassessment often relate changes in summary metrics that describe aspects of biotic assemblage structure and function to environmental stress. Biotic assessment using multimetric indices now forms the basis for setting regulatory standards for stream quality and a range of other goals related to water resource management in the USA and elsewhere. Biotic metrics are typically interpreted with reference to the expected natural state to evaluate whether a site is degraded. It is critical that natural variation in biotic metrics along environmental gradients is adequately accounted for, in order to quantify human disturbance-induced change. A common approach used in the IBI is to examine scatter plots of variation in a given metric along a single stream size surrogate and a fit a line (drawn by eye) to form the upper bound, and hence define the maximum likely value of a given metric in a site of a given environmental characteristic (termed the 'maximum species richness line' - MSRL). In this paper we examine whether the use of a single environmental descriptor and the MSRL is appropriate for defining the reference condition for a biotic metric (fish species richness) and for detecting human disturbance gradients in rivers of south-eastern Queensland, Australia. We compare the accuracy and precision of the MSRL approach based on single environmental predictors, with three regression-based prediction methods (Simple Linear Regression, Generalised Linear Modelling and Regression Tree modelling) that use (either singly or in combination) a set of landscape and local scale environmental variables as predictors of species richness. We compared the frequency of classification errors from each method against set biocriteria and contrast the ability of each method to accurately reflect human disturbance gradients at a large set of test sites. The results of this study suggest that the MSRL based upon variation in a single environmental descriptor could not accurately predict species richness at minimally disturbed sites when compared with SLR's based on equivalent environmental variables. Regression-based modelling incorporating multiple environmental variables as predictors more accurately explained natural variation in species richness than did simple models using single environmental predictors. Prediction error arising from the MSRL was substantially higher than for the regression methods and led to an increased frequency of Type I errors (incorrectly classing a site as disturbed). We suggest that problems with the MSRL arise from the inherent scoring procedure used and that it is limited to predicting variation in the dependent variable along a single environmental gradient.

A comparison of spatially explicit landscape representation methods and their relationship to stream condition

1. Biodiversity, water quality and ecosystem processes in streams are known to be influenced by the terrestrial landscape over a range of spatial and temporal scales. Lumped attributes (i.e. per cent land use) are often used to characterise the condition of the catchment; however, they are not spatially explicit and do not account for the disproportionate influence of land located near the stream or connected by overland flow. 2. We compared seven landscape representation metrics to determine whether accounting for the spatial proximity and hydrological effects of land use can be used to account for additional variability in indicators of stream ecosystem health. The landscape metrics included the following: a lumped metric, four inverse-distance-weighted (IDW) metrics based on distance to the stream or survey site and two modified IDW metrics that also accounted for the level of hydrologic activity (HA-IDW). Ecosystem health data were obtained from the Ecological Health Monitoring Programme in Southeast Queensland, Australia and included measures of fish, invertebrates, physicochemistry and nutrients collected during two seasons over 4 years. Linear models were fitted to the stream indicators and landscape metrics, by season, and compared using an information-theoretic approach. 3. Although no single metric was most suitable for modelling all stream indicators, lumped metrics rarely performed as well as other metric types. Metrics based on proximity to the stream (IDW and HA-IDW) were more suitable for modelling fish indicators, while the HA-IDW metric based on proximity to the survey site generally outperformed others for invertebrates, irrespective of season. There was consistent support for metrics based on proximity to the survey site (IDW or HA-IDW) for all physicochemical indicators during the dry season, while a HA-IDW metric based on proximity to the stream was suitable for five of the six physicochemical indicators in the post-wet season. Only one nutrient indicator was tested and results showed that catchment area had a significant effect on the relationship between land use metrics and algal stable isotope ratios in both seasons. 4. Spatially explicit methods of landscape representation can clearly improve the predictive ability of many empirical models currently used to study the relationship between landscape, habitat and stream condition. A comparison of different metrics may provide clues about causal pathways and mechanistic processes behind correlative relationships and could be used to target restoration efforts strategically.

A comparison of three models for mine water management

Water management is vital for mine sites both for production and sustainability related issues. Effective water management is a complex task since the role of water on mine sites is multifaceted. Computers models are tools that represent mine site water interaction and can be used by mine sites to inform or evaluate their water management strategies. There exist several types of models that can be used to represent mine site water interactions. This paper presents three such models: an operational model, an aggregated systems model and a generic systems model. For each model the paper provides a description and example followed by an analysis of its advantages and disadvantages. The paper hypotheses that since no model is optimal for all situations, each model should be applied in situations where it is most appropriate based upon the scale of water interactions being investigated, either unit (operation), inter-site (aggregated systems) or intra-site (generic systems).

A comparison of stability and bifurcation criteria for inflated spherical elastic shells

The nonlinear stability analysis introduced by Chen and Haughton [1] is employed to study the full nonlinear stability of the non-homogeneous spherically symmetric deformation of an elastic thick-walled sphere. The shell is composed of an arbitrary homogeneous, incompressible elastic material. The stability criterion ultimately requires the solution of a third-order nonlinear ordinary differential equation. Numerical calculations performed for a wide variety of well-known incompressible materials are then compared with existing bifurcation results and are found to be identical. Further analysis and comparison between stability and bifurcation are conducted for the case of thin shells and we prove by direct calculation that the two criteria are identical for all modes and all materials.

Guided ionization waves : theory and experiments

This review focuses on one of the fundamental phenomena that occur upon application of sufficiently strong electric fields to gases, namely the formation and propagation of ionization waves-streamers. The dynamics of streamers is controlled by strongly nonlinear coupling, in localized streamer tip regions, between enhanced (due to charge separation) electric field and ionization and transport of charged species in the enhanced field. Streamers appear in nature (as initial stages of sparks and lightning, as huge structures-sprites above thunderclouds), and are also found in numerous technological applications of electrical discharges. Here we discuss the fundamental physics of the guided streamer-like structures-plasma bullets which are produced in cold atmospheric-pressure plasma jets. Plasma bullets are guided ionization waves moving in a thin column of a jet of plasma forming gases (e.g.,He or Ar) expanding into ambient air. In contrast to streamers in a free (unbounded) space that propagate in a stochastic manner and often branch, guided ionization waves are repetitive and highly-reproducible and propagate along the same path-the jet axis. This property of guided streamers, in comparison with streamers in a free space, enables many advanced time-resolved experimental studies of ionization waves with nanosecond precision. In particular, experimental studies on manipulation of streamers by external electric fields and streamer interactions are critically examined. This review also introduces the basic theories and recent advances on the experimental and computational studies of guided streamers, in particular related to the propagation dynamics of ionization waves and the various parameters of relevance to plasma streamers. This knowledge is very useful to optimize the efficacy of applications of plasma streamer discharges in various fields ranging from health care and medicine to materials science and nanotechnology.

Current control in the magnetron systems for nanofabrication : a comparison

A cylindrical magnetron system and a hybrid inductively coupled plasma-assisted magnetron deposition system were examined experimentally in light of their discharge characteristics with a view to stress the enhanced controllability of the hybrid system. The comparative study has shown that the hybrid magnetron + the inductively coupled plasma system is a flexible, powerful, and convenient tool that has certain advantages as compared with the cylindrical dc magnetrons. In particular, the hybrid system features more linear current-voltage characteristics and the possibility of a bias-independent control of the discharge current.

Examining corporate governance disclosures of listed companies in Fiji

In 2009, the Capital Markets Development Authority (CMDA) - Fiji’s capital market regulator - introduced the Code of Corporate Governance (the Code). The Code is ‘principle-based’ and requires companies listed on the South Pacific Stock Exchange (SPSE) and the financial intermediaries to disclose their compliance with the Code’s principles. While compliance with the Code is mandatory, the nature and extent of disclosure is at the discretion of the complying entities. Agency theory and signalling theory suggest that firms with higher expected levels of agency costs will provide greater levels of voluntary disclosures as signals of strong corporate governance. Thus, the study seeks to test these theories by examining the heterogeneity of corporate governance disclosures by firms listed on SPSE, and determining the characteristics of firms that provide similar levels of disclosures. We conducted a content analysis of corporate governance disclosures on the annual reports of firms from 2008-2012. The study finds that large, non-family owned firms with high levels of shareholder dispersion provide greater quantity and higher quality corporate governance disclosures. For firms that are relatively smaller, family owned and have low levels of shareholder dispersion, the quantity and quality of corporate governance disclosures are much lower. Some of these firms provide boilerplate disclosures with minimal changes in the following years. These findings support the propositions of agency and signalling theory, which suggest that firms with higher separation between agents and principals will provide more voluntary disclosures to reduce expected agency costs transfers. Semi-structured interviews conducted with key stakeholders further reinforce the findings. The interviews also reveal that complying entities positively perceive the introduction of the Code. Furthermore, while compliance with Code brought about additional costs, they believed that most of these costs were minimal and one-off, and the benefits of greater corporate disclosure to improve user decision making outweighed the costs. The study contributes to the literature as it provides insight into the experience of a small capital market with introducing a ‘principle-based’ Code that attempts to encourage corporate governance practices through enhanced disclosure. The study also assists policy makers better understand complying entities’ motivations for compliance and the extent of compliance.

The alcohol culture of mature-aged women : similarities and differences across borders

Introduction: Relatively few attempts have been made to describe and understand women’s alcohol consumption beyond adolescence and young adulthood. In particular, there has been a lack of studies focusing on the alcohol culture that surrounds and guides mature-aged women’s drinking. As part of a larger cross-national comparison, the present study sought to address this gap by identifying the shared beliefs and values that impact on drinking outcomes among mature-aged women in Sweden and Australia. Method: The study was guided by an ethnographic methodology. To generate data, a series of semi-structured interview were conducted with 17 Australian (age = 45-57 years; M = 52.1, SD = 3.9) and 19 Swedish (age = 45-58 years; M = 52.2, SD = 4.8) women. All interviews were transcribed verbatim and thematically analysed. Results: With age, the focus of alcohol as a single purpose vehicle for intoxication had given way to a focus on the enjoyment and ritual of drinking itself; taste had become increasingly important and alcohol was strongly associated with pleasurable environments and experiences. The view of alcohol as a taste experience was particularly pronounced among the Swedish women, with alcohol (most commonly wine) often seen as inseparable from food. Among the Swedish women, this view of alcohol was also associated with a strong de-emphasis of the pharmacological effects of alcohol. In contrast, several Australian women understood and used alcohol as relief for anxiety and stress. Moderate drinking was linked to the social construction of both age and gender in the two samples, while heavy or abusive alcohol consumption was associated with strong proscriptive norms and stigma. Conclusions: Australian and Swedish women share a number of beliefs and values around alcohol, however, these findings also show unique country-level differences. Implications for drinking outcomes are discussed.

How thick SiO2 cap layer is needed to achieve strong visible photoluminescence from SiO2-buffered SiNx films?

The effect of a SiO2 nanolayer and annealing temperature on the UV/visible room-temperature photoluminescence (PL) from SiNx films synthesized by rf magnetron sputtering is studied. The PL intensity can be maximized when the SiO2 layer is 510 nm thick at 800 °C annealing temperature and only 2 nm at 1000 °C. A compositionstructureproperty analysis reveals that the PL intensity is directly related to both the surface chemical states and the content of the SiO and SiN bonds in the SiNx films. These results are relevant for the development of advanced optoelectronic and photonic emitters and sensors. © 2010 Elsevier B.V. All rights reserved.

Observations on the formation, growth and chemical composition of aerosols in an urban environment

The charge and chemical composition of ambient particles in an urban environment were determined using a Neutral Particle and Air Ion Spectrometer and an Aerodyne compact Time-Of-Flight Aerosol Mass Spectrometer. Particle formation and growth events were observed on 20 of the 36 days of sampling, with eight of these events classified as strong. During these events, peaks in the concentration of intermediate and large ions were followed by peaks in the concentration of ammonium and sulphate, which were not observed in the organic fraction. Comparison of days with and without particle formation events revealed that ammonium and sulphate were the dominant species on particle formation days while high concentrations of biomass burning OA inhibited particle growth. Analyses of the degree of particle neutralisation lead us to conclude that an excess of ammonium enabled particle formation and growth. In addition, the large ion concentration increased sharply during particle growth, suggesting that during nucleation the neutral gaseous species ammonia and sulphuric acid react to form ammonium and sulphate ions. Overall, we conclude that the mechanism of particle formation and growth involved ammonia and sulphuric acid, with limited input from organics.

Comparison of block and event-related experimental designs in diffusion-weighted functional MRI

PURPOSE To compare diffusion-weighted functional magnetic resonance imaging (DfMRI), a novel alternative to the blood oxygenation level-dependent (BOLD) contrast, in a functional MRI experiment. MATERIALS AND METHODS Nine participants viewed contrast reversing (7.5 Hz) black-and-white checkerboard stimuli using block and event-related paradigms. DfMRI (b = 1800 mm/s2 ) and BOLD sequences were acquired. Four parameters describing the observed signal were assessed: percent signal change, spatial extent of the activation, the Euclidean distance between peak voxel locations, and the time-to-peak of the best fitting impulse response for different paradigms and sequences. RESULTS The BOLD conditions showed a higher percent signal change relative to DfMRI; however, event-related DfMRI showed the strongest group activation (t = 21.23, P < 0.0005). Activation was more diffuse and spatially closer to the BOLD response for DfMRI when the block design was used. DfMRIevent showed the shortest TTP (4.4 +/- 0.88 sec). CONCLUSION The hemodynamic contribution to DfMRI may increase with the use of block designs.

Sense of home, sense of place : a morpho-typological comparative study of Florida and Queensland

Cities in the 21st century have become layered and complex systems not only in terms of physical form, but also social and cultural structure. Consolidated tools to analyze the urban environment have today to be improved including a strong interdisciplinary perspective in order to understand and manage the unprecedented complexity our cities are facing. Redevelopments, new estates, internal and external migrations are all dynamics which are deeply modifying the built environment directly or indirectly also affecting local identity, culture and social structure. This paper investigates the relationship between urban form and social behaviors, with particular attention to the perception of the built environment and its use by long term residents, recent migrants as well as tourists. A comparative study is suggested between South East Queensland and Florida; this two regions share common features such as subtropical climate, similar lifestyle, leisure cities and canal estates. Neighborhoods on the Gold and Sunshine Coasts have been designed using the communities of Florida, such as Celebration or Seaside, as models. These regions share also significant migration processes, similar social problems and high crime rates, which directly affect the local economies. Comparing Florida and SEQ could provide an understanding of different strategies adopted and how urban development and lifestyle can be managed maintaining social equity and security. This study, investigates people’s perception of built form and how this affects the use of public space. The relationship between built environment and social behaviour has been previously investigated, for example by environmental psychology; the innovation proposed by this research is to study the perception of place in leisure cities at multiple levels. Locals, migrants and tourists have different understanding of the built form in the same location; this understanding affects the use of space and the attitude to visit or avoid some precincts. The research methodology integrates traditional morpho-typological investigations with qualitative methods; data are collected in the first phase through online surveys about perception of urban forms. Findings guide then the selection of neighbourhoods to be investigated in detail through questionnaires and Nolli maps, specifying morphological regions as well as recurrent building typologies. A final phase includes interviews with selected stakeholders. Major urban projects are discussed addressing how they are used and perceived by locals, migrants or tourists; the comparison between SEQ and Florida allows the identification of strategies to address migration issues in both regions with particular attention to urban form and placemaking dynamics.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent