Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer-stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.

Response variation of optically stimulated luminescence dosimeters

Introduction This study investigates uncertainties pertaining to the use of optically stimulated luminescence dosimeters (OSLDs) in radiotherapy dosimetry. The sensitivity of the luminescent material is related to the density of recombination centres [1], which is in the range of 1015–1016 cm-3. Because of this non-uniform distribution of traps in crystal growth the sensitivity varies substantially within a batch of dosimeters. However, a quantitative understanding of the relationship between the response of an OSLD and its sensitive volume has not yet been investigated or reported in literature. Methods In this work, OSLDs are scanned with a MicroCT scanner to determine potential sources for the variation in relative sensitivity across a selection of Landauer nanoDot dosimeters. Specifically, the correlation between a dosimeters relative sensitivity and the loading density of Al2O3:C powder was determined. Results When extrapolating the sensitive volume’s radiodensity from the CT data, it was shown that there is a non-uniform distribution incrystal growth as illustrated in Fig. 1. A plot of voxel count versus the element-specific correction factor is shown in Fig. 2 where each point represents a single OSLD. A line was fitted which has an R2-value of 0.69 and a P-value of 8.21 9 10-19. This data shows that the response of a dosimeter decreases proportionally with sensitive volume. Extrapolating from this data, a quantitative relationship between response and sensitive volume was roughly determined for this batch of dosimeters. A change in volume of 1.176 9 10-5 cm3 corresponds to a 1 % change in response. In other words, a 0.05 % change in the nominal volume of the chip would result in a 1 % change in response. Discussion and conclusions This work demonstrated that the amount of sensitive material is approximately linked to the total correction factor. Furthermore, the ‘true’ volume of an OSLD’s sensitive material is, on average, 17.90 % less than that which has been reported in literature, mainly due to the presence of air cavities in the material’s structure. Finally, the potential effects of the inaccuracy of Al2O3:C deposition increases with decreasing chip size. If a luminescent dosimeter were manufactured with a smaller volume than currently employed using the same manufacturing protocol, the variation in response from chip to chip would more than likely exceed the current 5 % range.

Measurement of general and specific approaches to physical activity parenting : a systematic review

Background Parents play a significant role in shaping youth physical activity (PA). However, interventions targeting PA parenting have been ineffective. Methodological inconsistencies related to the measurement of parental influences may be a contributing factor. The purpose of this article is to review the extant peer-reviewed literature related to the measurement of general and specific parental influences on youth PA. Methods A systematic review of studies measuring constructs of PA parenting was conducted. Computerized searches were completed using PubMed, MEDLINE, Academic Search Premier, SPORTDiscus, and PsycINFO. Reference lists of the identified articles were manually reviewed as well as the authors' personal collections. Articles were selected on the basis of strict inclusion criteria and details regarding the measurement protocols were extracted. A total of 117 articles met the inclusionary criteria. Methodological articles that evaluated the validity and reliability of PA parenting measures (n=10) were reviewed separately from parental influence articles (n=107). Results A significant percentage of studies used measures with indeterminate validity and reliability. A significant percentage of articles did not provide sample items, describe the response format, or report the possible range of scores. No studies were located that evaluated sensitivity to change. Conclusion The reporting of measurement properties and the use of valid and reliable measurement scales need to be improved considerably.

Long-term persistence of tissue-engineered adipose flaps in a murine model to 1 year : an update

BACKGROUND Tissue engineering of patient-specific adipose tissue has the potential to revolutionize reconstructive surgery. Numerous models have been described for the production of adipose tissue with success in the short term, but little has been reported on the stability of this tissue-engineered fat beyond 4 months. METHODS A murine model of de novo adipogenesis producing a potentially transplantable adipose tissue flap within 4 to 6 weeks was developed in the authors' laboratory. In this study, the authors assess the ability of three-chamber (44-μl volume) configurations shown to be adipogenic in previous short-term studies (autograft, n = 8; open, n = 6; fat flap, n = 11) to maintain their tissue volume for up to 12 months in vivo, to determine the most adipogenic configuration in the long term. RESULTS Those chambers having the most contact with existing vascularized adipose tissue (open and fat flap groups) showed increased mean adipose tissue percentage (77 ± 5.6 percent and 81 ± 6.9 percent, respectively; p < 0.0007) and volume (12 ± 6.8 μl and 30 ± 14 μl, respectively; p < 0.025) when compared with short-term controls and greater adipose tissue volume than the autograft (sealed) chamber group (4.9 ± 5.8 μl; p = 0.0001) at 1 year. Inclusion of a vascularized fat flap within the chamber produced the best results, with new fat completely filling the chamber by 1 year. CONCLUSIONS These findings demonstrate that fat produced by tissue engineering is capable of maintaining its volume when the appropriate microenvironment is provided. This has important implications for the application of tissue-engineering techniques in humans.

"The Handbook of English for Specific Purposes" reviewed by Karen Woodman

English for specific purposes is a critical, but often under-researched, area in the fields of TESOL and Applied Linguistics, so the publication of a collection on this topic is a very positive development for those who work and/or research in the area.

An arteriovenous loop in a protected space generates a permanent, highly vascular, tissue-engineered construct

A major obstacle to 3-dimensional tissue engineering is incorporation of a functional vascular supply to support the expanding new tissue. This is overcome in an in vivo intrinsic vascularization model where an arteriovenous loop (AVL) is placed in a noncollapsible space protected by a polycarbonate chamber. Vascular development and hypoxia were examined from 3 days to 112 days by vascular casting, morphometric, and morphological techniques to understand the model's vascular growth and remodeling parameters for tissue engineering purposes. At 3 days a fibrin exudate surrounded the AVL, providing a scaffold to migrating inflammatory, endothelial, and mesenchymal cells. Capillaries formed between 3 and 7 days. Hypoxia and cell proliferation were maximal at 7 days, followed by a peak in percent vascular volume at 10 days (23.20±3.14% compared with 3.59±2.68% at 3 days, P<0.001). Maximal apoptosis was observed at 112 days. The protected space and spontaneous microcirculatory development in this model suggest it would be applicable for in vivo tissue engineering. A temporal window in a period of intense angiogenesis at 7 to 10 days is optimal for exogenous cell seeding and survival in the chamber, potentially enabling specific tissue outcomes to be achieved.

Spontaneous large volume adipose tissue generation from a vascularized pedicled fat flap inside a chamber space

A novel method of spontaneous generation of new adipose tissue from an existing fat flap is described. A defined volume of fat flap based on the superficial inferior epigastric vascular pedicle in the rat was elevated and inset into a hollow plastic chamber implanted subcutaneously in the groin of the rat. The chamber walls were either perforated or solid and the chambers either contained poly(D,L-lactic-co-glycolic acid) (PLGA) sponge matrix or not. The contents were analyzed after being in situ for 6 weeks. The total volume of the flap tissue in all groups except the control groups, where the flap was not inserted into the chambers, increased significantly, especially in the perforated chambers (0.08 ± 0.007 mL baseline compared to 1.2 ± 0.08 mL in the intact ones). Volume analysis of individual component tissues within the flaps revealed that the adipocyte volume increased and was at a maximum in the chambers without PLGA, where it expanded from 0.04 ± 0.003 mL at insertion to 0.5 ± 0.08 mL (1250% increase) in the perforated chambers and to 0.16 ± 0.03 mL (400% increase) in the intact chambers. Addition of PLGA scaffolds resulted in less fat growth. Histomorphometric analysis rather than simple hypertrophy documented an increased number of adipocytes. The new tissue was highly vascularized and no fat necrosis or atypical changes were observed.

Catchment-specific element signatures in estuarine crocodiles (Crocodylus porosus) from the Alligator Rivers Region, northern Australia

The concentrations of Na, K, Ca, Mg, Ba, Sr, Fe, Al, Mn, Zn, Pb, Cu, Ni, Cr, Co, Se, U and Ti were determined in the osteoderms and/or flesh of estuarine crocodiles (Crocodylus porosus) captured in three adjacent catchments within the Alligator Rivers Region (ARR) of northern Australia. Results from multivariate analysis of variance showed that when all metals were considered simultaneously, catchment effects were significant (P≤0.05). Despite considerable within-catchment variability, linear discriminant analysis (LDA) showed that differences in elemental signatures in the osteoderms and/or flesh of C. porosus amongst the catchments were sufficient to classify individuals accurately to their catchment of occurrence. Using cross-validation, the accuracy of classifying a crocodile to its catchment of occurrence was 76% for osteoderms and 60% for flesh. These data suggest that osteoderms provide better predictive accuracy than flesh for discriminating crocodiles amongst catchments. There was no advantage in combining the osteoderm and flesh results to increase the accuracy of classification (i.e. 67%). Based on the discriminant function coefficients for the osteoderm data, Ca, Co, Mg and U were the most important elements for discriminating amongst the three catchments. For flesh data, Ca, K, Mg, Na, Ni and Pb were the most important metals for discriminating amongst the catchments. Reasons for differences in the elemental signatures of crocodiles between catchments are generally not interpretable, due to limited data on surface water and sediment chemistry of the catchments or chemical composition of dietary items of C. porosus. From a wildlife management perspective, the provenance or source catchment(s) of 'problem' crocodiles captured at settlements or recreational areas along the ARR coastline may be established using catchment-specific elemental signatures. If the incidence of problem crocodiles can be reduced in settled or recreational areas by effective management at their source, then public safety concerns about these predators may be moderated, as well as the cost of their capture and removal. Copyright © 2002 Elsevier Science B.V.

Consumer acceptance of Accountable-eHealth systems

In this paper, we present the results of a survey conducted to measure the attitudes of the consumers of eHealth towards Accountable-eHealth systems which are designed for information privacy management. A research model is developed that can identify the factors contributing to system acceptance and is validated using quantitative data from 187 completed survey responses from university students studying non-health related courses at a university in Queensland, Australia. The research model is validated using structural equation modelling and can be used to identify how specific characteristics of Accountable-eHealth systems would affect their overall acceptance by future eHealth consumers.

A finite volume scheme with preconditioned Lanczos method for two-dimensional space-fractional reaction–diffusion equations

Fractional differential equations have been increasingly used as a powerful tool to model the non-locality and spatial heterogeneity inherent in many real-world problems. However, a constant challenge faced by researchers in this area is the high computational expense of obtaining numerical solutions of these fractional models, owing to the non-local nature of fractional derivatives. In this paper, we introduce a finite volume scheme with preconditioned Lanczos method as an attractive and high-efficiency approach for solving two-dimensional space-fractional reaction–diffusion equations. The computational heart of this approach is the efficient computation of a matrix-function-vector product f(A)bf(A)b, where A A is the matrix representation of the Laplacian obtained from the finite volume method and is non-symmetric. A key aspect of our proposed approach is that the popular Lanczos method for symmetric matrices is applied to this non-symmetric problem, after a suitable transformation. Furthermore, the convergence of the Lanczos method is greatly improved by incorporating a preconditioner. Our approach is show-cased by solving the fractional Fisher equation including a validation of the solution and an analysis of the behaviour of the model.

Crime, Justice and Social Democracy: Proceedings of the Second International Conference, 2013, volume 2

The refereed papers contained in this volume of conference proceedings were among those presented at the 2nd International Conference on Crime, Justice and Social Democracy, hosted by the Crime and Justice Research Centre, Faculty of Law, QUT, from 8 – 11 July 2013. The conference attracted an impressive list of speakers from Australasia, Europe, North America and Latin America. These seven papers can be viewed at the Crime and Justice Research Centre’s website at http://crimejusticeconference.com/publications/ as can Volume 1 representing another 26 selected papers from the conference. As with the papers contained in the first volume, this set of papers raises important questions about the links between crime, justice and social democracy, and continues the contribution that the Crime and Justice Research Centre makes towards engaging with these topics. We thank all those who submitted papers for review for this second volume of proceedings, as well as the peer reviewers for taking the time to review the papers, often within very tight timelines.

Audiencing through social media : a brief overview

Notwithstanding the problems with identifying audiences (c.f. Hartley, 1987), nor with sampling them (c.f. Turner, 2005), we contend that by using social media, it is at least possible to gain an understanding of the habits of those who chose to engage with content through social media. In this chapter, we will broadly outline the ways in which networks such as Twitter and Facebook can stand as proxies for audiences in a number of scenarios, and enable content creators, networks and researchers to understand the ways in which audiences come into existence, change over time, and engage with content. Beginning with the classic audience – television – we will consider the evolution of metrics from baseline volume metrics to the more sophisticated ‘telemetrics’ that are the focus of our current work. We discuss the evolution of these metrics, from principles developed in the field of ‘sabermetrics’, and highlight their effectiveness as both a predictor and a baseline for producers and networks to measure the success of their social media campaigns. Moving beyond the evaluation of the audiences engagement, we then move to consider the ‘audiences’ themselves. Building on Hartley’s argument that audiences are “imagined” constructs (1987, p. 125), we demonstrate the continual shift of Australian television audiences, from episode to episode and series to series, demonstrating through our map of the Australian Twittersphere (Bruns, Burgess & Highfield, 2014) both the variation amongst those who directly engage with television content, and those who are exposed to it through their social media networks. Finally, by exploring overlaps between sporting events (such as the NRL and AFL Grand Finals), reality TV (such as Big Brother, My Kitchen Rules & Biggest Loser), soaps (e.g. Bold & The Beautiful, Home & Away), and current affairs programming (e.g. Morning Television & A Current Affair), we discuss to what extent it is possible to profile and categorize Australian television audiences. Finally, we move beyond television audiences to consider audiences around social media platforms themselves. Building on our map of the Australian Twittersphere (Bruns, Burgess & Highfield, 2014), and a pool of 5000 active Australian accounts, we discuss the interconnectedness of audiences around particular subjects, and how specific topics spread throughout the Twitter Userbase. Also, by using Twitter as a proxy, we consider the career of a number of popular YouTuber’s, utilizing a method we refer to as Twitter Accession charts (Bruns & Woodford, 2014) to identify the growth curves, and relate them to specific events in the YouTubers career, be that ‘viral’ videos or collaborations, to discuss how audiences form around specific content creators.

Polarization of forecast densities : a new approach to time series classification

Time series classification has been extensively explored in many fields of study. Most methods are based on the historical or current information extracted from data. However, if interest is in a specific future time period, methods that directly relate to forecasts of time series are much more appropriate. An approach to time series classification is proposed based on a polarization measure of forecast densities of time series. By fitting autoregressive models, forecast replicates of each time series are obtained via the bias-corrected bootstrap, and a stationarity correction is considered when necessary. Kernel estimators are then employed to approximate forecast densities, and discrepancies of forecast densities of pairs of time series are estimated by a polarization measure, which evaluates the extent to which two densities overlap. Following the distributional properties of the polarization measure, a discriminant rule and a clustering method are proposed to conduct the supervised and unsupervised classification, respectively. The proposed methodology is applied to both simulated and real data sets, and the results show desirable properties.

Alternating current electrohydrodynamics induced nanoshearing and fluid micromixing for specific capture of cancer cells

We report a new tuneable alternating current (ac) electrohydrodynamics (ac-EHD) force referred to as “nanoshearing” which involves fluid flow generated within a few nanometers of an electrode surface. This force can be externally tuned via manipulating the applied ac-EHD field strength. The ability to manipulate ac-EHD induced forces and concomitant fluid micromixing can enhance fluid transport within the capture domain of the channel (e.g., transport of analytes and hence increase target–sensor interactions). This also provides a new capability to preferentially select strongly bound analytes over onspecifically bound cells and molecules. To demonstrate the utility and versatility of nanoshearing phenomenon to specifically capture cancer cells, we present proof-of-concept data in lysed blood using two microfluidic devices containing a long array of asymmetric planar electrode pairs. Under the optimal experimental conditions, we achieved high capture efficiency (e.g., approximately 90%; %RSD=2, n=3) with a 10-fold reduction in nonspecific dsorption of non-target cells for the detection of whole cells expressing Human Epidermal Growth Factor Receptor 2 (HER2). We believe that our ac-EHD devices and the use of tuneable nanoshearing phenomenon may find relevance in a wide variety of biological and medical applications.